Starting phenix.real_space_refine on Sun Mar 10 16:49:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpz_27644/03_2024/8dpz_27644.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpz_27644/03_2024/8dpz_27644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpz_27644/03_2024/8dpz_27644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpz_27644/03_2024/8dpz_27644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpz_27644/03_2024/8dpz_27644.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpz_27644/03_2024/8dpz_27644.pdb" } resolution = 3.38 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= -0.017 sd= 0.107 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 11 5.16 5 C 2115 2.51 5 N 551 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "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: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.36, per 1000 atoms: 0.71 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.28, 90.72, 74.52, 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 11 16.00 O 649 8.00 N 551 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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 F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 625.2 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 11.2% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.210A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.822A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN F 33 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.623A pdb=" N GLN F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.536A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR G 49 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 324 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: 0.90 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 898 1.46 - 1.58: 1458 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 3413 Sorted by residual: bond pdb=" C GLU G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.43e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C SER G 7 " pdb=" N PRO G 8 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" CB ASP F 100A" pdb=" CG ASP F 100A" ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 ... (remaining 3408 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.34: 121 107.34 - 114.03: 1802 114.03 - 120.73: 1369 120.73 - 127.43: 1316 127.43 - 134.12: 34 Bond angle restraints: 4642 Sorted by residual: angle pdb=" C ASP G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" N ASP F 100 " pdb=" CA ASP F 100 " pdb=" C ASP F 100 " ideal model delta sigma weight residual 109.95 105.91 4.04 1.44e+00 4.82e-01 7.86e+00 angle pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta sigma weight residual 120.06 123.39 -3.33 1.19e+00 7.06e-01 7.81e+00 angle pdb=" C PHE G 83 " pdb=" CA PHE G 83 " pdb=" CB PHE G 83 " ideal model delta sigma weight residual 111.31 115.81 -4.50 1.68e+00 3.54e-01 7.18e+00 angle pdb=" N TRP G 94 " pdb=" CA TRP G 94 " pdb=" C TRP G 94 " ideal model delta sigma weight residual 113.57 117.12 -3.55 1.38e+00 5.25e-01 6.62e+00 ... (remaining 4637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1822 16.50 - 33.01: 177 33.01 - 49.51: 25 49.51 - 66.02: 5 66.02 - 82.52: 4 Dihedral angle restraints: 2033 sinusoidal: 817 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.65 36.35 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA VAL F 95 " pdb=" C VAL F 95 " pdb=" N ALA F 96 " pdb=" CA ALA F 96 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN G 93 " pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 290 0.035 - 0.070: 137 0.070 - 0.106: 51 0.106 - 0.141: 19 0.141 - 0.176: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB THR G 102 " pdb=" CA THR G 102 " pdb=" OG1 THR G 102 " pdb=" CG2 THR G 102 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA TRP G 94 " pdb=" N TRP G 94 " pdb=" C TRP G 94 " pdb=" CB TRP G 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 498 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 79 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO B 337 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 83 " -0.014 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE G 83 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1186 2.87 - 3.38: 2663 3.38 - 3.89: 5282 3.89 - 4.39: 5920 4.39 - 4.90: 10828 Nonbonded interactions: 25879 Sorted by model distance: nonbonded pdb=" OH TYR F 97 " pdb=" OE1 GLU F 99 " model vdw 2.363 2.440 nonbonded pdb=" OD2 ASP B 405 " pdb=" OG SER G 30 " model vdw 2.408 2.440 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.420 2.520 nonbonded pdb=" OD1 ASP F 100 " pdb=" N ASP F 100A" model vdw 2.427 2.520 nonbonded pdb=" NH1 ARG G 61 " pdb=" OD2 ASP G 82 " model vdw 2.429 2.520 ... (remaining 25874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.430 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.042 3413 Z= 0.260 Angle : 0.772 8.142 4642 Z= 0.412 Chirality : 0.050 0.176 501 Planarity : 0.007 0.069 595 Dihedral : 13.012 82.522 1248 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.38), residues: 412 helix: -4.20 (0.35), residues: 27 sheet: -0.08 (0.45), residues: 139 loop : -1.92 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 103 HIS 0.001 0.001 HIS B 519 PHE 0.037 0.003 PHE G 83 TYR 0.018 0.002 TYR G 49 ARG 0.006 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.384 Fit side-chains REVERT: B 406 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 417 LYS cc_start: 0.8402 (tppt) cc_final: 0.8171 (tptt) REVERT: F 48 ILE cc_start: 0.8306 (mm) cc_final: 0.7982 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2175 time to fit residues: 16.5273 Evaluate side-chains 55 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3413 Z= 0.200 Angle : 0.558 5.041 4642 Z= 0.294 Chirality : 0.044 0.152 501 Planarity : 0.005 0.053 595 Dihedral : 5.044 24.587 510 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.28 % Allowed : 7.50 % Favored : 92.22 % 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: -1.58 (0.39), residues: 412 helix: -3.70 (0.60), residues: 21 sheet: 0.30 (0.46), residues: 140 loop : -1.70 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.000 0.000 HIS B 519 PHE 0.021 0.002 PHE G 83 TYR 0.010 0.001 TYR G 49 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.382 Fit side-chains REVERT: B 417 LYS cc_start: 0.8523 (tppt) cc_final: 0.8246 (tptt) REVERT: F 48 ILE cc_start: 0.8448 (mm) cc_final: 0.8204 (mm) REVERT: F 100 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7253 (tm-30) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2223 time to fit residues: 16.5134 Evaluate side-chains 58 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3413 Z= 0.224 Angle : 0.586 11.319 4642 Z= 0.304 Chirality : 0.045 0.151 501 Planarity : 0.004 0.044 595 Dihedral : 4.854 21.536 510 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.94 % Allowed : 9.44 % Favored : 88.61 % 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: -1.42 (0.40), residues: 412 helix: -3.29 (0.68), residues: 28 sheet: 0.30 (0.46), residues: 138 loop : -1.44 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.019 0.002 PHE G 83 TYR 0.012 0.001 TYR F 100F ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.382 Fit side-chains REVERT: B 417 LYS cc_start: 0.8555 (tppt) cc_final: 0.8221 (tppt) REVERT: B 418 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7637 (mt) REVERT: F 48 ILE cc_start: 0.8472 (mm) cc_final: 0.8259 (mm) REVERT: F 100 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7212 (tm-30) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.2116 time to fit residues: 15.4560 Evaluate side-chains 63 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3413 Z= 0.166 Angle : 0.539 9.414 4642 Z= 0.279 Chirality : 0.044 0.145 501 Planarity : 0.004 0.047 595 Dihedral : 4.575 19.602 510 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.67 % Allowed : 11.39 % Favored : 86.94 % 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: -1.31 (0.40), residues: 412 helix: -2.59 (0.94), residues: 21 sheet: 0.30 (0.46), residues: 138 loop : -1.46 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 94 HIS 0.000 0.000 HIS B 519 PHE 0.016 0.001 PHE G 83 TYR 0.010 0.001 TYR F 100F ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.397 Fit side-chains REVERT: B 417 LYS cc_start: 0.8535 (tppt) cc_final: 0.8210 (tppt) REVERT: F 48 ILE cc_start: 0.8486 (mm) cc_final: 0.8265 (mm) REVERT: F 100 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7076 (tm-30) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1923 time to fit residues: 13.7708 Evaluate side-chains 62 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3413 Z= 0.243 Angle : 0.584 9.193 4642 Z= 0.300 Chirality : 0.045 0.155 501 Planarity : 0.004 0.044 595 Dihedral : 4.696 20.006 510 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.17 % Allowed : 10.00 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.40), residues: 412 helix: -2.40 (1.01), residues: 21 sheet: 0.30 (0.46), residues: 138 loop : -1.47 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.016 0.002 PHE F 78 TYR 0.013 0.001 TYR F 100F ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.378 Fit side-chains REVERT: B 347 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: B 417 LYS cc_start: 0.8568 (tppt) cc_final: 0.8249 (tppt) REVERT: F 100 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7171 (tm-30) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 0.1842 time to fit residues: 14.1286 Evaluate side-chains 64 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3413 Z= 0.231 Angle : 0.577 8.987 4642 Z= 0.297 Chirality : 0.045 0.155 501 Planarity : 0.004 0.044 595 Dihedral : 4.698 19.673 510 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.89 % Allowed : 10.56 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.40), residues: 412 helix: -2.45 (1.01), residues: 21 sheet: 0.32 (0.46), residues: 138 loop : -1.46 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE F 78 TYR 0.013 0.001 TYR F 100F ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.342 Fit side-chains REVERT: B 347 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: B 376 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8628 (p) REVERT: B 417 LYS cc_start: 0.8553 (tppt) cc_final: 0.8208 (tppt) REVERT: F 82 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7767 (mp) REVERT: F 100 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7143 (tm-30) outliers start: 14 outliers final: 9 residues processed: 64 average time/residue: 0.1609 time to fit residues: 12.4042 Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.0270 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3413 Z= 0.217 Angle : 0.571 8.732 4642 Z= 0.293 Chirality : 0.045 0.153 501 Planarity : 0.004 0.044 595 Dihedral : 4.642 19.547 510 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.17 % Allowed : 11.39 % Favored : 84.44 % 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: -1.29 (0.40), residues: 412 helix: -2.36 (1.03), residues: 21 sheet: 0.31 (0.46), residues: 138 loop : -1.46 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.016 0.002 PHE F 78 TYR 0.012 0.001 TYR F 100F ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.387 Fit side-chains REVERT: B 347 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: B 376 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 417 LYS cc_start: 0.8544 (tppt) cc_final: 0.8201 (tppt) REVERT: F 82 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7752 (mp) REVERT: F 100 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7115 (tm-30) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.1916 time to fit residues: 15.0355 Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.7943 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3413 Z= 0.414 Angle : 0.696 10.017 4642 Z= 0.358 Chirality : 0.049 0.192 501 Planarity : 0.005 0.043 595 Dihedral : 5.210 21.761 510 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.89 % Allowed : 11.94 % Favored : 84.17 % 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: 412 helix: -3.36 (0.66), residues: 34 sheet: -0.00 (0.49), residues: 125 loop : -1.77 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 34 HIS 0.001 0.001 HIS B 519 PHE 0.022 0.003 PHE F 78 TYR 0.020 0.002 TYR F 100F ARG 0.003 0.001 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.388 Fit side-chains REVERT: B 417 LYS cc_start: 0.8605 (tppt) cc_final: 0.8237 (tppt) REVERT: F 82 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7851 (mp) REVERT: F 99 GLU cc_start: 0.8315 (tt0) cc_final: 0.8074 (tt0) REVERT: F 100 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7340 (tm-30) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.1630 time to fit residues: 12.7618 Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7894 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3413 Z= 0.231 Angle : 0.596 8.808 4642 Z= 0.306 Chirality : 0.046 0.159 501 Planarity : 0.004 0.042 595 Dihedral : 4.952 23.872 510 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.89 % Allowed : 13.61 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.39), residues: 412 helix: -2.94 (0.83), residues: 28 sheet: 0.09 (0.49), residues: 125 loop : -1.49 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE F 78 TYR 0.015 0.001 TYR F 100F ARG 0.004 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.350 Fit side-chains REVERT: B 376 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8606 (p) REVERT: B 417 LYS cc_start: 0.8541 (tppt) cc_final: 0.8243 (tptt) REVERT: F 82 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7824 (mp) REVERT: F 99 GLU cc_start: 0.8296 (tt0) cc_final: 0.8004 (tt0) REVERT: F 100 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7250 (tm-30) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.1716 time to fit residues: 12.9010 Evaluate side-chains 66 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7887 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3413 Z= 0.222 Angle : 0.596 8.518 4642 Z= 0.305 Chirality : 0.045 0.154 501 Planarity : 0.004 0.042 595 Dihedral : 4.843 25.528 510 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.89 % Allowed : 13.89 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.40), residues: 412 helix: -2.89 (0.83), residues: 28 sheet: 0.15 (0.49), residues: 126 loop : -1.39 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE F 78 TYR 0.015 0.001 TYR F 100F ARG 0.003 0.000 ARG B 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.360 Fit side-chains REVERT: B 376 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8595 (p) REVERT: B 417 LYS cc_start: 0.8535 (tppt) cc_final: 0.8168 (tppt) REVERT: F 82 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7827 (mp) REVERT: F 100 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7193 (tm-30) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.1675 time to fit residues: 12.3913 Evaluate side-chains 64 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.118756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099212 restraints weight = 5118.836| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3413 Z= 0.216 Angle : 0.586 8.387 4642 Z= 0.299 Chirality : 0.045 0.149 501 Planarity : 0.004 0.042 595 Dihedral : 4.770 26.734 510 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.61 % Allowed : 14.72 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.40), residues: 412 helix: -2.80 (0.84), residues: 28 sheet: 0.23 (0.49), residues: 126 loop : -1.33 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.001 PHE F 78 TYR 0.014 0.001 TYR F 100F ARG 0.003 0.000 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.12 seconds wall clock time: 23 minutes 34.75 seconds (1414.75 seconds total)