Starting phenix.real_space_refine on Sun Mar 10 18:09:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/03_2024/7p14_13155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/03_2024/7p14_13155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/03_2024/7p14_13155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/03_2024/7p14_13155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/03_2024/7p14_13155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/03_2024/7p14_13155_updated.pdb" } resolution = 3.66 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= 0.002 sd= 0.046 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 25 5.16 5 C 2533 2.51 5 N 579 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" 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: 3796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2706 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PLC': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 2.93, per 1000 atoms: 0.77 Number of scatterers: 3796 At special positions: 0 Unit cell: (96.348, 69.006, 70.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 3 15.00 O 656 8.00 N 579 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " 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 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 690.8 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 61.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.515A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 66 removed outlier: 3.741A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.530A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 157 removed outlier: 3.590A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 3.572A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.504A pdb=" N ARG A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 5.032A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 removed outlier: 3.654A pdb=" N LEU A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 249 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.733A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 307 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.616A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.725A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 678 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: 1.03 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 545 1.32 - 1.44: 1168 1.44 - 1.56: 2136 1.56 - 1.69: 6 1.69 - 1.81: 37 Bond restraints: 3892 Sorted by residual: bond pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" C3 P5S A 403 " pdb=" O16 P5S A 403 " ideal model delta sigma weight residual 1.405 1.456 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C4 PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" C4 PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 PLC A 402 " pdb=" O3P PLC A 402 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 3887 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.77: 39 104.77 - 112.09: 1914 112.09 - 119.40: 1221 119.40 - 126.72: 2040 126.72 - 134.04: 56 Bond angle restraints: 5270 Sorted by residual: angle pdb=" O3P PLC A 402 " pdb=" P PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 93.62 104.20 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 103.08 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C3 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 107.38 114.66 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" CA LYS A 284 " pdb=" CB LYS A 284 " pdb=" CG LYS A 284 " ideal model delta sigma weight residual 114.10 118.68 -4.58 2.00e+00 2.50e-01 5.24e+00 angle pdb=" CA LEU A 330 " pdb=" CB LEU A 330 " pdb=" CG LEU A 330 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.65e+00 ... (remaining 5265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2092 27.26 - 54.52: 135 54.52 - 81.77: 21 81.77 - 109.03: 5 109.03 - 136.29: 3 Dihedral angle restraints: 2256 sinusoidal: 927 harmonic: 1329 Sorted by residual: dihedral pdb=" O2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O3P PLC A 401 " ideal model delta sinusoidal sigma weight residual 304.29 168.00 136.29 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O3P PLC A 401 " ideal model delta sinusoidal sigma weight residual 67.16 -58.95 126.11 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C27 P5S A 403 " pdb=" C28 P5S A 403 " pdb=" C29 P5S A 403 " pdb=" C30 P5S A 403 " ideal model delta sinusoidal sigma weight residual -179.38 -65.29 -114.09 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 2253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 508 0.053 - 0.106: 74 0.106 - 0.159: 4 0.159 - 0.213: 0 0.213 - 0.266: 1 Chirality restraints: 587 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.05 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" C PRO A 201 " pdb=" CB PRO A 201 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 584 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 319 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 320 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 200 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 201 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 33 " -0.005 2.00e-02 2.50e+03 9.48e-03 8.99e-01 pdb=" C ASN B 33 " 0.016 2.00e-02 2.50e+03 pdb=" O ASN B 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE B 34 " -0.005 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1091 2.82 - 3.34: 3686 3.34 - 3.86: 5967 3.86 - 4.38: 7145 4.38 - 4.90: 12071 Nonbonded interactions: 29960 Sorted by model distance: nonbonded pdb=" OE1 GLU A 260 " pdb=" NH2 ARG A 264 " model vdw 2.295 2.520 nonbonded pdb=" O ILE A 16 " pdb=" OG1 THR A 20 " model vdw 2.369 2.440 nonbonded pdb=" OH TYR A 182 " pdb=" O LEU A 371 " model vdw 2.372 2.440 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.393 2.440 nonbonded pdb=" OH TYR A 208 " pdb=" OH TYR A 291 " model vdw 2.419 2.440 ... (remaining 29955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 1.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 0.051 3892 Z= 0.305 Angle : 0.638 10.583 5270 Z= 0.289 Chirality : 0.037 0.266 587 Planarity : 0.004 0.064 624 Dihedral : 18.548 136.288 1407 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.40), residues: 444 helix: 1.37 (0.31), residues: 257 sheet: 1.11 (0.70), residues: 52 loop : -0.55 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.005 0.001 PHE A 225 TYR 0.015 0.001 TYR A 340 ARG 0.002 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.420 Fit side-chains REVERT: A 139 THR cc_start: 0.9153 (m) cc_final: 0.8884 (p) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1390 time to fit residues: 12.8744 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.0060 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3892 Z= 0.193 Angle : 0.565 6.571 5270 Z= 0.282 Chirality : 0.038 0.145 587 Planarity : 0.004 0.039 624 Dihedral : 16.386 130.841 612 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.76 % Allowed : 6.05 % Favored : 92.19 % 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: 2.10 (0.39), residues: 444 helix: 2.44 (0.30), residues: 258 sheet: 1.00 (0.69), residues: 52 loop : -0.56 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.001 0.000 HIS A 101 PHE 0.036 0.002 PHE A 94 TYR 0.015 0.001 TYR A 182 ARG 0.002 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.417 Fit side-chains REVERT: A 50 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7417 (m) REVERT: A 139 THR cc_start: 0.9102 (m) cc_final: 0.8824 (p) REVERT: B 121 TYR cc_start: 0.7268 (p90) cc_final: 0.5943 (p90) REVERT: B 127 GLN cc_start: 0.8556 (tp40) cc_final: 0.8300 (tp-100) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.1295 time to fit residues: 12.6893 Evaluate side-chains 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3892 Z= 0.163 Angle : 0.502 5.450 5270 Z= 0.249 Chirality : 0.038 0.166 587 Planarity : 0.003 0.030 624 Dihedral : 14.675 127.553 612 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.52 % Allowed : 9.07 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.39), residues: 444 helix: 2.88 (0.29), residues: 261 sheet: 1.00 (0.68), residues: 52 loop : -0.61 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 245 HIS 0.001 0.000 HIS A 82 PHE 0.023 0.001 PHE A 104 TYR 0.012 0.001 TYR A 182 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.410 Fit side-chains REVERT: A 7 ASN cc_start: 0.8933 (t0) cc_final: 0.8694 (m-40) REVERT: A 37 GLN cc_start: 0.8760 (mt0) cc_final: 0.8559 (mt0) REVERT: A 97 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8168 (mtm-85) REVERT: A 139 THR cc_start: 0.8980 (m) cc_final: 0.8704 (p) REVERT: B 121 TYR cc_start: 0.7228 (p90) cc_final: 0.5864 (p90) REVERT: B 127 GLN cc_start: 0.8549 (tp40) cc_final: 0.8289 (tp-100) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.1368 time to fit residues: 13.1269 Evaluate side-chains 70 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.0020 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3892 Z= 0.160 Angle : 0.490 5.418 5270 Z= 0.244 Chirality : 0.037 0.167 587 Planarity : 0.003 0.029 624 Dihedral : 13.958 124.820 612 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.77 % Allowed : 10.58 % Favored : 86.65 % 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: 2.79 (0.40), residues: 444 helix: 3.13 (0.29), residues: 261 sheet: 1.03 (0.68), residues: 52 loop : -0.58 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 56 PHE 0.018 0.001 PHE A 199 TYR 0.012 0.001 TYR A 182 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.421 Fit side-chains REVERT: A 37 GLN cc_start: 0.8743 (mt0) cc_final: 0.8524 (mt0) REVERT: A 139 THR cc_start: 0.8943 (m) cc_final: 0.8678 (p) REVERT: A 265 LEU cc_start: 0.8496 (tp) cc_final: 0.8268 (tt) REVERT: A 366 ARG cc_start: 0.5652 (ttm170) cc_final: 0.5439 (ttm-80) REVERT: B 121 TYR cc_start: 0.7327 (p90) cc_final: 0.5901 (p90) REVERT: B 127 GLN cc_start: 0.8571 (tp40) cc_final: 0.8300 (tp-100) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.1396 time to fit residues: 12.8003 Evaluate side-chains 74 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3892 Z= 0.249 Angle : 0.532 5.986 5270 Z= 0.264 Chirality : 0.039 0.181 587 Planarity : 0.003 0.025 624 Dihedral : 13.998 125.141 612 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.27 % Allowed : 11.08 % Favored : 85.64 % 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: 2.80 (0.40), residues: 444 helix: 3.18 (0.29), residues: 260 sheet: 0.99 (0.67), residues: 52 loop : -0.62 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.001 0.000 HIS A 56 PHE 0.021 0.001 PHE A 8 TYR 0.014 0.001 TYR B 121 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.430 Fit side-chains REVERT: A 37 GLN cc_start: 0.8797 (mt0) cc_final: 0.8577 (mt0) REVERT: A 265 LEU cc_start: 0.8659 (tp) cc_final: 0.8363 (tt) REVERT: A 284 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7734 (tttt) REVERT: B 127 GLN cc_start: 0.8588 (tp40) cc_final: 0.8289 (tp-100) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.1330 time to fit residues: 13.1147 Evaluate side-chains 75 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3892 Z= 0.215 Angle : 0.521 6.002 5270 Z= 0.260 Chirality : 0.038 0.182 587 Planarity : 0.003 0.025 624 Dihedral : 13.836 125.149 612 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.77 % Allowed : 12.85 % Favored : 84.38 % 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: 2.74 (0.40), residues: 444 helix: 3.13 (0.29), residues: 260 sheet: 0.97 (0.67), residues: 52 loop : -0.63 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 121 PHE 0.015 0.001 PHE A 8 TYR 0.014 0.001 TYR B 121 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8773 (mt0) cc_final: 0.8558 (mt0) REVERT: A 284 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7490 (tttt) REVERT: B 127 GLN cc_start: 0.8577 (tp40) cc_final: 0.8274 (tp-100) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.1487 time to fit residues: 13.4092 Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7536 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3892 Z= 0.168 Angle : 0.501 6.114 5270 Z= 0.251 Chirality : 0.037 0.183 587 Planarity : 0.002 0.022 624 Dihedral : 13.519 124.015 612 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.27 % Allowed : 13.10 % Favored : 83.63 % 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: 2.66 (0.40), residues: 444 helix: 3.07 (0.29), residues: 265 sheet: 1.00 (0.67), residues: 52 loop : -0.89 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 245 HIS 0.001 0.000 HIS A 56 PHE 0.015 0.001 PHE A 104 TYR 0.014 0.001 TYR A 340 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.413 Fit side-chains REVERT: A 37 GLN cc_start: 0.8746 (mt0) cc_final: 0.8524 (mt0) REVERT: A 264 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7660 (ttm170) REVERT: A 265 LEU cc_start: 0.8529 (tp) cc_final: 0.8244 (tt) REVERT: A 284 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7449 (tttt) REVERT: B 127 GLN cc_start: 0.8552 (tp40) cc_final: 0.8248 (tp-100) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.1538 time to fit residues: 14.2563 Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 12 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3892 Z= 0.206 Angle : 0.528 6.248 5270 Z= 0.263 Chirality : 0.038 0.187 587 Planarity : 0.002 0.018 624 Dihedral : 13.484 123.643 612 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.27 % Allowed : 13.60 % Favored : 83.12 % 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: 2.67 (0.40), residues: 444 helix: 3.13 (0.29), residues: 263 sheet: 1.01 (0.67), residues: 52 loop : -0.95 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 93 HIS 0.001 0.000 HIS A 101 PHE 0.016 0.001 PHE A 94 TYR 0.013 0.001 TYR B 121 ARG 0.007 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.407 Fit side-chains REVERT: A 37 GLN cc_start: 0.8767 (mt0) cc_final: 0.8540 (mt0) REVERT: A 199 PHE cc_start: 0.7734 (t80) cc_final: 0.7344 (t80) REVERT: A 264 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7734 (ttm170) REVERT: A 265 LEU cc_start: 0.8526 (tp) cc_final: 0.8244 (tt) REVERT: A 284 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7748 (tttt) REVERT: B 127 GLN cc_start: 0.8558 (tp40) cc_final: 0.8260 (tp-100) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.1320 time to fit residues: 12.0510 Evaluate side-chains 74 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7584 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3892 Z= 0.235 Angle : 0.540 6.302 5270 Z= 0.269 Chirality : 0.039 0.192 587 Planarity : 0.003 0.029 624 Dihedral : 13.455 123.853 612 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.27 % Allowed : 14.11 % Favored : 82.62 % 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: 2.70 (0.40), residues: 444 helix: 3.14 (0.29), residues: 263 sheet: 1.00 (0.67), residues: 52 loop : -0.90 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 104 TYR 0.013 0.001 TYR B 121 ARG 0.007 0.001 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.433 Fit side-chains REVERT: A 37 GLN cc_start: 0.8794 (mt0) cc_final: 0.8579 (mt0) REVERT: A 199 PHE cc_start: 0.7801 (t80) cc_final: 0.7411 (t80) REVERT: A 260 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 264 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7727 (ttm170) REVERT: A 265 LEU cc_start: 0.8646 (tp) cc_final: 0.8342 (tt) REVERT: B 127 GLN cc_start: 0.8542 (tp40) cc_final: 0.8223 (tp-100) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.1333 time to fit residues: 12.7541 Evaluate side-chains 74 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3892 Z= 0.214 Angle : 0.541 6.327 5270 Z= 0.270 Chirality : 0.038 0.193 587 Planarity : 0.003 0.023 624 Dihedral : 13.307 123.635 612 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.02 % Allowed : 14.36 % Favored : 82.62 % 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: 2.81 (0.40), residues: 444 helix: 3.28 (0.29), residues: 258 sheet: 0.91 (0.66), residues: 52 loop : -0.71 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 104 TYR 0.018 0.001 TYR A 340 ARG 0.007 0.001 ARG A 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.424 Fit side-chains REVERT: A 37 GLN cc_start: 0.8783 (mt0) cc_final: 0.8551 (mt0) REVERT: A 199 PHE cc_start: 0.7808 (t80) cc_final: 0.7403 (t80) REVERT: A 260 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6386 (tm-30) REVERT: A 264 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7684 (ttm170) REVERT: A 265 LEU cc_start: 0.8638 (tp) cc_final: 0.8328 (tt) REVERT: B 127 GLN cc_start: 0.8536 (tp40) cc_final: 0.8194 (tp-100) outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.1350 time to fit residues: 12.7073 Evaluate side-chains 77 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131360 restraints weight = 4405.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134638 restraints weight = 2946.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136758 restraints weight = 2260.999| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3892 Z= 0.244 Angle : 0.558 6.344 5270 Z= 0.278 Chirality : 0.039 0.199 587 Planarity : 0.003 0.025 624 Dihedral : 13.265 123.870 612 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.27 % Allowed : 13.85 % Favored : 82.87 % 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: 2.79 (0.40), residues: 444 helix: 3.25 (0.29), residues: 258 sheet: 0.89 (0.65), residues: 52 loop : -0.69 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.018 0.001 PHE A 104 TYR 0.017 0.001 TYR A 340 ARG 0.006 0.000 ARG A 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.09 seconds wall clock time: 20 minutes 33.78 seconds (1233.78 seconds total)