Starting phenix.real_space_refine on Thu Nov 14 05:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g5k_51088/11_2024/9g5k_51088.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g5k_51088/11_2024/9g5k_51088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g5k_51088/11_2024/9g5k_51088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g5k_51088/11_2024/9g5k_51088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g5k_51088/11_2024/9g5k_51088.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g5k_51088/11_2024/9g5k_51088.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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 20 5.16 5 C 2674 2.51 5 N 633 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 991 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain: "A" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3035 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.21, per 1000 atoms: 1.29 Number of scatterers: 4040 At special positions: 0 Unit cell: (87.15, 80.51, 80.51, 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 20 16.00 O 713 8.00 N 633 7.00 C 2674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 45 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 566.6 milliseconds 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 67.3% alpha, 13.2% 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 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 56 through 77 removed outlier: 4.329A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.694A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 4.182A pdb=" N TYR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.502A pdb=" N ASN A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.699A pdb=" N TYR A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.316A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.667A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 425 removed outlier: 3.881A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.136A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.506A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.384A pdb=" N TYR B 32 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG B 52 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 283 hydrogen bonds defined for protein. 810 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: 1.14 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 878 1.33 - 1.45: 1042 1.45 - 1.57: 2198 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4152 Sorted by residual: bond pdb=" CA GLN B 39 " pdb=" C GLN B 39 " ideal model delta sigma weight residual 1.520 1.476 0.044 1.12e-02 7.97e+03 1.53e+01 bond pdb=" CA ASN A 340 " pdb=" C ASN A 340 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" N GLN B 39 " pdb=" CA GLN B 39 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.20e-02 6.94e+03 8.22e+00 bond pdb=" CA ASN A 399 " pdb=" C ASN A 399 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.37e-02 5.33e+03 8.10e+00 bond pdb=" CA PRO B 41 " pdb=" C PRO B 41 " ideal model delta sigma weight residual 1.521 1.491 0.030 1.27e-02 6.20e+03 5.75e+00 ... (remaining 4147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 5510 1.66 - 3.32: 128 3.32 - 4.98: 20 4.98 - 6.63: 2 6.63 - 8.29: 1 Bond angle restraints: 5661 Sorted by residual: angle pdb=" C GLN B 39 " pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " ideal model delta sigma weight residual 110.24 104.46 5.78 1.46e+00 4.69e-01 1.56e+01 angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 110.80 119.09 -8.29 2.13e+00 2.20e-01 1.52e+01 angle pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 120.79 117.90 2.89 9.70e-01 1.06e+00 8.88e+00 angle pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" C TRP A 94 " ideal model delta sigma weight residual 111.82 115.07 -3.25 1.16e+00 7.43e-01 7.84e+00 angle pdb=" C ALA B 40 " pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta sigma weight residual 119.76 116.91 2.85 1.03e+00 9.43e-01 7.68e+00 ... (remaining 5656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2095 16.35 - 32.70: 203 32.70 - 49.04: 67 49.04 - 65.39: 14 65.39 - 81.74: 5 Dihedral angle restraints: 2384 sinusoidal: 887 harmonic: 1497 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.11 33.89 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" C GLN B 39 " pdb=" N GLN B 39 " pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" N LEU B 11 " pdb=" CA LEU B 11 " pdb=" CB LEU B 11 " pdb=" CG LEU B 11 " ideal model delta sinusoidal sigma weight residual -60.00 -117.11 57.11 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 537 0.053 - 0.107: 91 0.107 - 0.160: 13 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 645 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG A 78 " pdb=" N ARG A 78 " pdb=" C ARG A 78 " pdb=" CB ARG A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 642 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.112 2.00e-02 2.50e+03 9.32e-02 1.09e+02 pdb=" C7 NAG A 601 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.083 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 40 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ALA B 40 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA B 40 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 41 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 339 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C VAL A 339 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 339 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 340 " -0.009 2.00e-02 2.50e+03 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1033 2.79 - 3.32: 3914 3.32 - 3.85: 6972 3.85 - 4.37: 8161 4.37 - 4.90: 14160 Nonbonded interactions: 34240 Sorted by model distance: nonbonded pdb=" O MET A 384 " pdb=" OG1 THR A 388 " model vdw 2.263 3.040 nonbonded pdb=" O LEU A 415 " pdb=" OG1 THR A 419 " model vdw 2.287 3.040 nonbonded pdb=" O LEU A 177 " pdb=" OG SER A 181 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.333 3.040 nonbonded pdb=" O TRP A 12 " pdb=" OG1 THR A 16 " model vdw 2.367 3.040 ... (remaining 34235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.490 Find NCS groups from input model: 0.040 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 0.049 4152 Z= 0.275 Angle : 0.605 8.292 5661 Z= 0.363 Chirality : 0.043 0.266 645 Planarity : 0.005 0.093 690 Dihedral : 15.279 81.741 1427 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.70 % Allowed : 15.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.37), residues: 501 helix: 1.97 (0.30), residues: 294 sheet: -0.23 (0.60), residues: 53 loop : 0.15 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.008 0.001 PHE A 279 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.436 Fit side-chains REVERT: B 89 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6769 (mp0) outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 1.1876 time to fit residues: 99.5526 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4152 Z= 0.277 Angle : 0.626 8.954 5661 Z= 0.326 Chirality : 0.043 0.159 645 Planarity : 0.004 0.034 690 Dihedral : 5.481 56.805 587 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.99 % Allowed : 14.32 % Favored : 81.69 % 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: 1.93 (0.37), residues: 501 helix: 2.12 (0.29), residues: 298 sheet: -0.14 (0.59), residues: 59 loop : 0.23 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.002 PHE A 279 TYR 0.018 0.002 TYR B 113 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.472 Fit side-chains REVERT: B 89 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 78 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.5481 (mpt-90) REVERT: A 166 ASN cc_start: 0.8070 (t0) cc_final: 0.7830 (t0) REVERT: A 349 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6974 (tp) outliers start: 17 outliers final: 5 residues processed: 87 average time/residue: 1.1573 time to fit residues: 104.4050 Evaluate side-chains 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4152 Z= 0.218 Angle : 0.558 7.992 5661 Z= 0.294 Chirality : 0.041 0.148 645 Planarity : 0.004 0.030 690 Dihedral : 5.284 54.236 585 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.23 % Allowed : 16.20 % Favored : 79.58 % 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: 2.14 (0.37), residues: 501 helix: 2.23 (0.29), residues: 301 sheet: 0.09 (0.58), residues: 59 loop : 0.34 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.012 0.001 PHE A 439 TYR 0.015 0.002 TYR A 280 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.436 Fit side-chains REVERT: B 19 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6511 (ttm-80) REVERT: A 166 ASN cc_start: 0.8009 (t0) cc_final: 0.7718 (t0) REVERT: A 440 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7872 (tp) outliers start: 18 outliers final: 8 residues processed: 89 average time/residue: 1.0334 time to fit residues: 95.6903 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 30 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4152 Z= 0.174 Angle : 0.538 7.742 5661 Z= 0.282 Chirality : 0.040 0.147 645 Planarity : 0.003 0.025 690 Dihedral : 4.223 17.753 582 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.05 % Allowed : 17.84 % Favored : 79.11 % 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: 2.29 (0.37), residues: 501 helix: 2.31 (0.29), residues: 301 sheet: 0.21 (0.57), residues: 59 loop : 0.46 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.013 0.001 PHE A 279 TYR 0.018 0.001 TYR A 280 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.454 Fit side-chains REVERT: A 166 ASN cc_start: 0.7963 (t0) cc_final: 0.7667 (t0) REVERT: A 278 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7112 (tt) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 1.0402 time to fit residues: 91.9710 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4152 Z= 0.336 Angle : 0.640 8.396 5661 Z= 0.336 Chirality : 0.045 0.157 645 Planarity : 0.004 0.026 690 Dihedral : 4.818 20.768 582 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.99 % Allowed : 16.43 % Favored : 79.58 % 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: 1.90 (0.37), residues: 501 helix: 1.96 (0.29), residues: 300 sheet: 0.09 (0.59), residues: 59 loop : 0.40 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.003 0.001 HIS A 135 PHE 0.016 0.002 PHE A 439 TYR 0.018 0.002 TYR A 280 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.411 Fit side-chains REVERT: A 166 ASN cc_start: 0.8001 (t0) cc_final: 0.7681 (t0) REVERT: A 278 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7280 (tt) outliers start: 17 outliers final: 9 residues processed: 86 average time/residue: 1.1408 time to fit residues: 101.7823 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4152 Z= 0.282 Angle : 0.610 8.995 5661 Z= 0.319 Chirality : 0.043 0.152 645 Planarity : 0.004 0.027 690 Dihedral : 4.864 25.093 582 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.23 % Allowed : 16.67 % Favored : 79.11 % 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: 1.87 (0.37), residues: 501 helix: 1.95 (0.29), residues: 300 sheet: 0.08 (0.60), residues: 59 loop : 0.37 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 PHE 0.017 0.002 PHE A 279 TYR 0.019 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.459 Fit side-chains REVERT: A 166 ASN cc_start: 0.8001 (t0) cc_final: 0.7685 (t0) REVERT: A 278 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7258 (tt) outliers start: 18 outliers final: 9 residues processed: 85 average time/residue: 1.0704 time to fit residues: 94.5209 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4152 Z= 0.235 Angle : 0.588 9.307 5661 Z= 0.308 Chirality : 0.042 0.153 645 Planarity : 0.004 0.027 690 Dihedral : 4.751 23.997 582 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.69 % Allowed : 16.43 % Favored : 78.87 % 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: 2.04 (0.37), residues: 501 helix: 2.06 (0.29), residues: 300 sheet: 0.25 (0.59), residues: 59 loop : 0.44 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 94 HIS 0.001 0.000 HIS A 200 PHE 0.012 0.002 PHE A 439 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.415 Fit side-chains REVERT: B 19 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6533 (tmm-80) REVERT: B 89 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 166 ASN cc_start: 0.7973 (t0) cc_final: 0.7657 (t0) REVERT: A 197 MET cc_start: 0.7543 (mtm) cc_final: 0.7299 (ttm) REVERT: A 278 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7211 (tt) REVERT: A 459 TYR cc_start: 0.2802 (OUTLIER) cc_final: 0.2153 (m-10) outliers start: 20 outliers final: 9 residues processed: 84 average time/residue: 1.1290 time to fit residues: 98.4746 Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4152 Z= 0.266 Angle : 0.608 9.303 5661 Z= 0.318 Chirality : 0.042 0.154 645 Planarity : 0.004 0.027 690 Dihedral : 4.792 24.450 582 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.23 % Allowed : 16.67 % Favored : 79.11 % 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: 2.00 (0.37), residues: 501 helix: 2.03 (0.29), residues: 300 sheet: 0.27 (0.59), residues: 59 loop : 0.40 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.024 0.002 PHE A 279 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.446 Fit side-chains REVERT: B 19 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6537 (tmm-80) REVERT: B 89 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: A 166 ASN cc_start: 0.7962 (t0) cc_final: 0.7666 (t0) REVERT: A 197 MET cc_start: 0.7530 (mtm) cc_final: 0.7303 (ttm) REVERT: A 278 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7271 (tt) REVERT: A 459 TYR cc_start: 0.3160 (OUTLIER) cc_final: 0.2390 (m-10) outliers start: 18 outliers final: 9 residues processed: 84 average time/residue: 1.0675 time to fit residues: 93.1303 Evaluate side-chains 88 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4152 Z= 0.270 Angle : 0.614 9.803 5661 Z= 0.320 Chirality : 0.042 0.156 645 Planarity : 0.004 0.027 690 Dihedral : 4.798 24.348 582 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.99 % Allowed : 18.08 % Favored : 77.93 % 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 (0.37), residues: 501 helix: 2.00 (0.29), residues: 300 sheet: 0.26 (0.59), residues: 59 loop : 0.39 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 200 PHE 0.014 0.002 PHE A 439 TYR 0.020 0.002 TYR A 280 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.496 Fit side-chains REVERT: B 19 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6510 (tmm-80) REVERT: B 89 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: A 166 ASN cc_start: 0.7944 (t0) cc_final: 0.7654 (t0) REVERT: A 278 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 459 TYR cc_start: 0.3010 (OUTLIER) cc_final: 0.2280 (m-10) outliers start: 17 outliers final: 9 residues processed: 80 average time/residue: 1.0777 time to fit residues: 89.7518 Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4152 Z= 0.236 Angle : 0.596 9.451 5661 Z= 0.309 Chirality : 0.042 0.154 645 Planarity : 0.004 0.027 690 Dihedral : 4.659 22.826 582 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.52 % Allowed : 18.54 % Favored : 77.93 % 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: 2.07 (0.37), residues: 501 helix: 2.08 (0.29), residues: 300 sheet: 0.30 (0.59), residues: 59 loop : 0.43 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.032 0.002 PHE A 279 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.475 Fit side-chains REVERT: B 19 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6519 (tmm-80) REVERT: A 166 ASN cc_start: 0.7919 (t0) cc_final: 0.7637 (t0) REVERT: A 278 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7279 (tt) REVERT: A 459 TYR cc_start: 0.2931 (OUTLIER) cc_final: 0.2456 (m-10) outliers start: 15 outliers final: 9 residues processed: 82 average time/residue: 1.0675 time to fit residues: 91.0271 Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.159679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.143255 restraints weight = 4840.562| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.29 r_work: 0.3419 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4152 Z= 0.260 Angle : 0.611 9.676 5661 Z= 0.318 Chirality : 0.042 0.154 645 Planarity : 0.004 0.027 690 Dihedral : 4.699 22.659 582 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.29 % Allowed : 19.25 % Favored : 77.46 % 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: 2.01 (0.37), residues: 501 helix: 2.04 (0.29), residues: 299 sheet: 0.28 (0.59), residues: 59 loop : 0.43 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.037 0.002 PHE A 279 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.11 seconds wall clock time: 44 minutes 28.25 seconds (2668.25 seconds total)