Starting phenix.real_space_refine on Sun Mar 10 16:18:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvj_34129/03_2024/7yvj_34129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvj_34129/03_2024/7yvj_34129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvj_34129/03_2024/7yvj_34129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvj_34129/03_2024/7yvj_34129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvj_34129/03_2024/7yvj_34129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvj_34129/03_2024/7yvj_34129.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2073 2.51 5 N 552 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B PHE 515": "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: 3267 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1491 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.35, per 1000 atoms: 0.72 Number of scatterers: 3267 At special positions: 0 Unit cell: (72.16, 68.88, 82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 626 8.00 N 552 7.00 C 2073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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: 1.30 Conformation dependent library (CDL) restraints added in 615.9 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 7.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.697A pdb=" N ASP C 31 " --> pdb=" O MET C 28 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 32 " --> pdb=" O ILE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.571A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 5.578A pdb=" N VAL A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 5.578A pdb=" N VAL A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.863A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.057A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 97 hydrogen bonds defined for protein. 216 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: 0.88 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 535 1.31 - 1.44: 1009 1.44 - 1.56: 1788 1.56 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3352 Sorted by residual: bond pdb=" CA ASN B 437 " pdb=" C ASN B 437 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.35e-02 5.49e+03 2.23e+01 bond pdb=" CA VAL B 350 " pdb=" C VAL B 350 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.22e-02 6.72e+03 2.04e+01 bond pdb=" C VAL B 350 " pdb=" O VAL B 350 " ideal model delta sigma weight residual 1.237 1.192 0.044 1.13e-02 7.83e+03 1.54e+01 bond pdb=" C ASN B 437 " pdb=" O ASN B 437 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.17e-02 7.31e+03 1.54e+01 bond pdb=" CA SER B 438 " pdb=" C SER B 438 " ideal model delta sigma weight residual 1.526 1.475 0.050 1.28e-02 6.10e+03 1.54e+01 ... (remaining 3347 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.14: 118 107.14 - 113.94: 1760 113.94 - 120.75: 1430 120.75 - 127.55: 1224 127.55 - 134.35: 28 Bond angle restraints: 4560 Sorted by residual: angle pdb=" C ALA B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 119.64 125.83 -6.19 1.01e+00 9.80e-01 3.75e+01 angle pdb=" N TRP B 353 " pdb=" CA TRP B 353 " pdb=" C TRP B 353 " ideal model delta sigma weight residual 110.24 117.26 -7.02 1.30e+00 5.92e-01 2.91e+01 angle pdb=" N ASN B 354 " pdb=" CA ASN B 354 " pdb=" C ASN B 354 " ideal model delta sigma weight residual 109.59 118.06 -8.47 1.61e+00 3.86e-01 2.77e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 119.76 -9.95 2.21e+00 2.05e-01 2.03e+01 angle pdb=" N TYR B 351 " pdb=" CA TYR B 351 " pdb=" C TYR B 351 " ideal model delta sigma weight residual 113.19 118.37 -5.18 1.19e+00 7.06e-01 1.89e+01 ... (remaining 4555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 1720 15.89 - 31.78: 196 31.78 - 47.67: 38 47.67 - 63.56: 5 63.56 - 79.45: 2 Dihedral angle restraints: 1961 sinusoidal: 731 harmonic: 1230 Sorted by residual: dihedral pdb=" N ASN B 439 " pdb=" C ASN B 439 " pdb=" CA ASN B 439 " pdb=" CB ASN B 439 " ideal model delta harmonic sigma weight residual 122.80 113.87 8.93 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CA GLN A 40 " pdb=" C GLN A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA THR A 72 " pdb=" C THR A 72 " pdb=" N ALA A 73 " pdb=" CA ALA A 73 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 392 0.080 - 0.160: 77 0.160 - 0.239: 8 0.239 - 0.319: 5 0.319 - 0.399: 2 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA TYR C 104 " pdb=" N TYR C 104 " pdb=" C TYR C 104 " pdb=" CB TYR C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA ALA B 372 " pdb=" N ALA B 372 " pdb=" C ALA B 372 " pdb=" CB ALA B 372 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA TRP B 353 " pdb=" N TRP B 353 " pdb=" C TRP B 353 " pdb=" CB TRP B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 481 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 420 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" CG ASP B 420 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP B 420 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 420 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 436 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C TRP B 436 " 0.050 2.00e-02 2.50e+03 pdb=" O TRP B 436 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN B 437 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 350 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C VAL B 350 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 350 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 351 " 0.013 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 22 2.42 - 3.04: 2156 3.04 - 3.66: 4751 3.66 - 4.28: 6698 4.28 - 4.90: 11578 Nonbonded interactions: 25205 Sorted by model distance: nonbonded pdb=" O GLN A 16 " pdb=" CD1 LEU A 80 " model vdw 1.805 3.460 nonbonded pdb=" OH TYR C 105 " pdb=" ND2 ASN B 354 " model vdw 2.023 2.520 nonbonded pdb=" O GLY B 476 " pdb=" OD1 ASN B 477 " model vdw 2.099 3.040 nonbonded pdb=" O SER C 30 " pdb=" OD1 ASP C 31 " model vdw 2.150 3.040 nonbonded pdb=" O GLY B 446 " pdb=" OH TYR B 449 " model vdw 2.190 2.440 ... (remaining 25200 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: 5.900 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: 26.490 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 0.064 3352 Z= 0.540 Angle : 1.049 9.948 4560 Z= 0.678 Chirality : 0.070 0.399 484 Planarity : 0.005 0.037 594 Dihedral : 13.624 79.449 1171 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.29 % Favored : 90.52 % Rotamer: Outliers : 1.73 % Allowed : 9.80 % Favored : 88.47 % 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: -4.50 (0.32), residues: 422 helix: -5.27 (0.23), residues: 29 sheet: -2.27 (0.36), residues: 153 loop : -3.28 (0.31), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.003 0.002 HIS A 41 PHE 0.008 0.001 PHE A 102 TYR 0.021 0.002 TYR C 104 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7487 (t0) cc_final: 0.7170 (t0) REVERT: C 13 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8451 (mmmt) REVERT: C 98 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7424 (tmt170) REVERT: C 100 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7810 (tp-100) REVERT: B 386 LYS cc_start: 0.7757 (mttt) cc_final: 0.7221 (pttt) outliers start: 6 outliers final: 1 residues processed: 124 average time/residue: 0.2075 time to fit residues: 29.5297 Evaluate side-chains 99 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 41 HIS B 354 ASN B 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.224 Angle : 0.654 7.399 4560 Z= 0.336 Chirality : 0.045 0.144 484 Planarity : 0.005 0.042 594 Dihedral : 5.524 57.328 479 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.45 % Favored : 94.08 % Rotamer: Outliers : 4.61 % Allowed : 16.14 % Favored : 79.25 % 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: -3.63 (0.34), residues: 422 helix: -5.19 (0.21), residues: 22 sheet: -1.62 (0.37), residues: 154 loop : -2.76 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 353 HIS 0.002 0.001 HIS A 41 PHE 0.015 0.001 PHE C 68 TYR 0.024 0.002 TYR B 508 ARG 0.007 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7971 (p90) cc_final: 0.7313 (p90) REVERT: A 55 ASN cc_start: 0.7857 (t0) cc_final: 0.7246 (t0) REVERT: C 13 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8526 (mmmt) REVERT: C 98 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7069 (tmt170) REVERT: C 99 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6677 (mt-10) REVERT: B 386 LYS cc_start: 0.7715 (mttt) cc_final: 0.7264 (ttpt) REVERT: B 403 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8462 (ttm-80) REVERT: B 508 TYR cc_start: 0.8458 (m-80) cc_final: 0.8009 (m-80) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 0.2069 time to fit residues: 27.4797 Evaluate side-chains 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.223 Angle : 0.631 5.893 4560 Z= 0.319 Chirality : 0.044 0.144 484 Planarity : 0.005 0.067 594 Dihedral : 5.296 56.515 479 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.69 % Favored : 94.08 % Rotamer: Outliers : 6.63 % Allowed : 19.60 % Favored : 73.78 % 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: -2.97 (0.35), residues: 422 helix: -5.08 (0.29), residues: 22 sheet: -1.10 (0.38), residues: 154 loop : -2.32 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.024 0.001 TYR C 80 ARG 0.012 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8103 (p90) cc_final: 0.7264 (p90) REVERT: A 55 ASN cc_start: 0.7843 (t0) cc_final: 0.7082 (t0) REVERT: A 100 TYR cc_start: 0.8446 (m-80) cc_final: 0.8083 (m-80) REVERT: C 13 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8377 (mmmt) REVERT: C 34 MET cc_start: 0.9265 (mmt) cc_final: 0.9062 (mmp) REVERT: C 99 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6779 (mt-10) REVERT: B 358 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9144 (tp) REVERT: B 386 LYS cc_start: 0.7468 (mttt) cc_final: 0.7073 (ttpt) REVERT: B 498 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7908 (mtt-85) REVERT: B 508 TYR cc_start: 0.8412 (m-80) cc_final: 0.8159 (m-80) outliers start: 23 outliers final: 19 residues processed: 109 average time/residue: 0.1945 time to fit residues: 24.8373 Evaluate side-chains 115 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.189 Angle : 0.600 6.082 4560 Z= 0.300 Chirality : 0.043 0.142 484 Planarity : 0.005 0.046 594 Dihedral : 5.063 54.993 479 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 7.20 % Allowed : 20.46 % Favored : 72.33 % 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: -2.44 (0.37), residues: 422 helix: -4.64 (0.44), residues: 16 sheet: -0.75 (0.39), residues: 156 loop : -2.05 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.002 0.000 HIS A 41 PHE 0.013 0.001 PHE B 400 TYR 0.025 0.001 TYR C 80 ARG 0.008 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8039 (p90) cc_final: 0.7161 (p90) REVERT: A 55 ASN cc_start: 0.7822 (t0) cc_final: 0.7445 (t0) REVERT: C 13 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8581 (mmmt) REVERT: B 386 LYS cc_start: 0.7258 (mttt) cc_final: 0.6898 (ttpt) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.1832 time to fit residues: 23.7496 Evaluate side-chains 115 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3352 Z= 0.228 Angle : 0.621 6.375 4560 Z= 0.318 Chirality : 0.044 0.153 484 Planarity : 0.005 0.044 594 Dihedral : 5.114 54.613 479 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 6.92 % Allowed : 22.19 % Favored : 70.89 % 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: -2.28 (0.37), residues: 422 helix: -4.48 (0.57), residues: 16 sheet: -0.48 (0.40), residues: 152 loop : -2.06 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.002 0.001 HIS A 41 PHE 0.013 0.001 PHE C 68 TYR 0.026 0.001 TYR B 508 ARG 0.010 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8109 (p90) cc_final: 0.7186 (p90) REVERT: A 55 ASN cc_start: 0.7901 (t0) cc_final: 0.7541 (t0) REVERT: C 13 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8620 (mmmt) REVERT: C 98 ARG cc_start: 0.8056 (ttt-90) cc_final: 0.7551 (tmm-80) REVERT: B 386 LYS cc_start: 0.7199 (mttt) cc_final: 0.6785 (ttpt) outliers start: 24 outliers final: 21 residues processed: 106 average time/residue: 0.1820 time to fit residues: 22.8060 Evaluate side-chains 110 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3352 Z= 0.177 Angle : 0.613 6.587 4560 Z= 0.307 Chirality : 0.043 0.142 484 Planarity : 0.004 0.041 594 Dihedral : 4.911 52.817 479 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.74 % Favored : 95.02 % Rotamer: Outliers : 6.92 % Allowed : 22.48 % Favored : 70.61 % 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: -1.97 (0.38), residues: 422 helix: -4.31 (0.69), residues: 16 sheet: -0.09 (0.42), residues: 144 loop : -1.93 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE B 400 TYR 0.016 0.001 TYR C 80 ARG 0.011 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8068 (p90) cc_final: 0.7227 (p90) REVERT: A 55 ASN cc_start: 0.7868 (t0) cc_final: 0.7500 (t0) REVERT: C 13 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8623 (mmmt) REVERT: C 65 LYS cc_start: 0.8384 (tppp) cc_final: 0.8079 (tppt) REVERT: B 386 LYS cc_start: 0.7240 (mttt) cc_final: 0.6828 (ttpt) outliers start: 24 outliers final: 16 residues processed: 110 average time/residue: 0.1892 time to fit residues: 24.3334 Evaluate side-chains 112 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8137 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3352 Z= 0.220 Angle : 0.654 11.104 4560 Z= 0.319 Chirality : 0.043 0.156 484 Planarity : 0.004 0.050 594 Dihedral : 4.991 52.684 479 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.69 % Favored : 94.08 % Rotamer: Outliers : 7.20 % Allowed : 23.34 % Favored : 69.45 % 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: -1.85 (0.39), residues: 422 helix: -3.67 (1.00), residues: 16 sheet: -0.08 (0.42), residues: 152 loop : -1.89 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 115 HIS 0.002 0.001 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.013 0.001 TYR C 80 ARG 0.013 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8131 (p90) cc_final: 0.7259 (p90) REVERT: A 55 ASN cc_start: 0.8020 (t0) cc_final: 0.7618 (t0) REVERT: B 386 LYS cc_start: 0.7112 (mttt) cc_final: 0.6735 (ttpt) outliers start: 25 outliers final: 24 residues processed: 107 average time/residue: 0.1869 time to fit residues: 23.4130 Evaluate side-chains 117 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0060 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3352 Z= 0.211 Angle : 0.669 11.151 4560 Z= 0.321 Chirality : 0.043 0.145 484 Planarity : 0.005 0.052 594 Dihedral : 4.955 52.237 479 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 6.05 % Allowed : 24.50 % Favored : 69.45 % 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: -1.77 (0.40), residues: 422 helix: -3.82 (0.90), residues: 16 sheet: -0.00 (0.42), residues: 152 loop : -1.83 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 115 HIS 0.002 0.000 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.013 0.001 TYR C 80 ARG 0.012 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8134 (p90) cc_final: 0.7510 (p90) REVERT: A 55 ASN cc_start: 0.8123 (t0) cc_final: 0.7497 (t0) REVERT: C 34 MET cc_start: 0.9004 (mmp) cc_final: 0.8762 (mmp) REVERT: B 386 LYS cc_start: 0.7086 (mttt) cc_final: 0.6722 (ttpt) outliers start: 21 outliers final: 21 residues processed: 111 average time/residue: 0.1891 time to fit residues: 24.5381 Evaluate side-chains 116 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3352 Z= 0.180 Angle : 0.658 7.792 4560 Z= 0.320 Chirality : 0.043 0.147 484 Planarity : 0.005 0.063 594 Dihedral : 4.862 50.742 479 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.69 % Favored : 94.08 % Rotamer: Outliers : 6.63 % Allowed : 23.92 % Favored : 69.45 % 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: -1.65 (0.40), residues: 422 helix: -4.07 (0.76), residues: 16 sheet: 0.21 (0.44), residues: 144 loop : -1.76 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE B 400 TYR 0.015 0.001 TYR C 80 ARG 0.013 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8056 (p90) cc_final: 0.7468 (p90) REVERT: A 55 ASN cc_start: 0.8134 (t0) cc_final: 0.7430 (t0) REVERT: B 386 LYS cc_start: 0.7048 (mttt) cc_final: 0.6701 (ttpt) outliers start: 23 outliers final: 22 residues processed: 108 average time/residue: 0.1793 time to fit residues: 22.7360 Evaluate side-chains 116 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3352 Z= 0.372 Angle : 0.759 9.122 4560 Z= 0.379 Chirality : 0.046 0.139 484 Planarity : 0.005 0.066 594 Dihedral : 5.550 54.236 479 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.24 % Favored : 90.52 % Rotamer: Outliers : 7.49 % Allowed : 23.05 % Favored : 69.45 % 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: -1.99 (0.39), residues: 422 helix: -4.58 (0.47), residues: 16 sheet: -0.13 (0.42), residues: 152 loop : -1.95 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 115 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.002 PHE C 68 TYR 0.015 0.002 TYR C 56 ARG 0.014 0.001 ARG A 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8245 (p90) cc_final: 0.7754 (p90) REVERT: A 55 ASN cc_start: 0.8338 (t0) cc_final: 0.7751 (t0) outliers start: 26 outliers final: 24 residues processed: 102 average time/residue: 0.1641 time to fit residues: 19.9269 Evaluate side-chains 110 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080289 restraints weight = 8339.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082658 restraints weight = 3765.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084186 restraints weight = 2116.051| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.181 Angle : 0.714 10.619 4560 Z= 0.339 Chirality : 0.044 0.147 484 Planarity : 0.005 0.055 594 Dihedral : 5.002 50.779 479 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 6.34 % Allowed : 25.07 % Favored : 68.59 % 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 (0.40), residues: 422 helix: -4.57 (0.49), residues: 16 sheet: 0.05 (0.42), residues: 152 loop : -1.82 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.001 PHE B 400 TYR 0.015 0.001 TYR C 80 ARG 0.014 0.001 ARG A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1501.25 seconds wall clock time: 27 minutes 43.04 seconds (1663.04 seconds total)