Starting phenix.real_space_refine on Fri Aug 2 14:26:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/08_2024/8xv9_38693.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/08_2024/8xv9_38693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/08_2024/8xv9_38693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/08_2024/8xv9_38693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/08_2024/8xv9_38693.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/08_2024/8xv9_38693.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 17 5.16 5 C 2127 2.51 5 N 472 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3147 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3110 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.79, per 1000 atoms: 0.89 Number of scatterers: 3147 At special positions: 0 Unit cell: (67.41, 70.62, 77.04, 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 17 16.00 O 531 8.00 N 472 7.00 C 2127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.27 Conformation dependent library (CDL) restraints added in 615.6 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.765A pdb=" N TYR A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.915A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.705A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.833A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 removed outlier: 3.829A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.586A pdb=" N SER A 129 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 130' Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 168 through 189 removed outlier: 4.087A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 307 removed outlier: 5.277A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 335 Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.616A pdb=" N VAL A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.513A pdb=" N CYS A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 426 removed outlier: 3.848A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 459 removed outlier: 3.574A pdb=" N GLN A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 891 1.35 - 1.47: 974 1.47 - 1.59: 1351 1.59 - 1.72: 0 1.72 - 1.84: 30 Bond restraints: 3246 Sorted by residual: bond pdb=" CAQ 2TA A 501 " pdb=" CAR 2TA A 501 " ideal model delta sigma weight residual 1.526 1.343 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" CAT 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.456 1.285 0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" CAQ 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.454 1.583 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NBE 2TA A 501 " pdb=" SBD 2TA A 501 " ideal model delta sigma weight residual 1.639 1.757 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " ideal model delta sigma weight residual 1.361 1.475 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 3241 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 87 106.82 - 113.61: 1732 113.61 - 120.41: 1364 120.41 - 127.20: 1218 127.20 - 134.00: 36 Bond angle restraints: 4437 Sorted by residual: angle pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" CAG 2TA A 501 " ideal model delta sigma weight residual 131.32 114.42 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C4 2TA A 501 " pdb=" NAW 2TA A 501 " pdb=" CAX 2TA A 501 " ideal model delta sigma weight residual 131.24 120.10 11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ILE A 36 " pdb=" C ILE A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 118.88 123.77 -4.89 1.54e+00 4.22e-01 1.01e+01 angle pdb=" OBJ 2TA A 501 " pdb=" SBD 2TA A 501 " pdb=" OBK 2TA A 501 " ideal model delta sigma weight residual 118.13 109.12 9.01 3.00e+00 1.11e-01 9.01e+00 angle pdb=" N TYR A 14 " pdb=" CA TYR A 14 " pdb=" C TYR A 14 " ideal model delta sigma weight residual 109.81 115.94 -6.13 2.21e+00 2.05e-01 7.71e+00 ... (remaining 4432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.97: 1801 28.97 - 57.95: 22 57.95 - 86.92: 7 86.92 - 115.90: 2 115.90 - 144.87: 1 Dihedral angle restraints: 1833 sinusoidal: 681 harmonic: 1152 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CAG 2TA A 501 " pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sinusoidal sigma weight residual -0.72 -145.59 144.87 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 1830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 292 0.035 - 0.071: 148 0.071 - 0.106: 45 0.106 - 0.141: 13 0.141 - 0.176: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TYR A 14 " pdb=" N TYR A 14 " pdb=" C TYR A 14 " pdb=" CB TYR A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 499 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " 0.018 2.00e-02 2.50e+03 1.64e-02 5.38e+00 pdb=" CG TYR A 373 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 29 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 30 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 61 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C TYR A 61 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR A 61 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 62 " -0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1181 2.90 - 3.40: 3062 3.40 - 3.90: 5208 3.90 - 4.40: 5520 4.40 - 4.90: 9624 Nonbonded interactions: 24595 Sorted by model distance: nonbonded pdb=" OE1 GLU A 32 " pdb=" NAW 2TA A 501 " model vdw 2.402 3.120 nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.412 3.040 nonbonded pdb=" O PHE A 22 " pdb=" OG SER A 26 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.476 3.040 nonbonded pdb=" O LYS A 270 " pdb=" OG SER A 274 " model vdw 2.485 3.040 ... (remaining 24590 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.183 3246 Z= 0.526 Angle : 0.936 16.896 4437 Z= 0.449 Chirality : 0.047 0.176 502 Planarity : 0.007 0.051 529 Dihedral : 12.311 144.871 1097 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.31), residues: 384 helix: -1.68 (0.22), residues: 279 sheet: None (None), residues: 0 loop : -3.83 (0.44), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 59 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.041 0.002 TYR A 373 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.7605 (p) cc_final: 0.7084 (m) REVERT: A 36 ILE cc_start: 0.7864 (tp) cc_final: 0.7439 (tp) REVERT: A 77 VAL cc_start: 0.7653 (m) cc_final: 0.7315 (t) REVERT: A 115 MET cc_start: 0.6896 (ttp) cc_final: 0.6562 (ttp) REVERT: A 152 THR cc_start: 0.7629 (m) cc_final: 0.7115 (p) REVERT: A 306 LYS cc_start: 0.6487 (mmtt) cc_final: 0.6262 (mmtt) REVERT: A 364 HIS cc_start: 0.6529 (t70) cc_final: 0.6234 (t-90) REVERT: A 369 ILE cc_start: 0.8050 (tp) cc_final: 0.7687 (tp) REVERT: A 389 ILE cc_start: 0.7768 (mt) cc_final: 0.7465 (mt) REVERT: A 423 VAL cc_start: 0.7605 (t) cc_final: 0.7056 (m) REVERT: A 440 LEU cc_start: 0.7185 (tp) cc_final: 0.6565 (mt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1198 time to fit residues: 14.9575 Evaluate side-chains 79 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 10 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 173 ASN A 294 GLN A 356 ASN A 364 HIS ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3246 Z= 0.250 Angle : 0.661 6.252 4437 Z= 0.343 Chirality : 0.043 0.157 502 Planarity : 0.005 0.042 529 Dihedral : 13.701 155.494 440 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.60 % Allowed : 11.71 % Favored : 87.69 % 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: -0.57 (0.41), residues: 384 helix: 0.47 (0.29), residues: 284 sheet: None (None), residues: 0 loop : -2.78 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.026 0.002 PHE A 439 TYR 0.029 0.002 TYR A 126 ARG 0.001 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7518 (tp) REVERT: A 77 VAL cc_start: 0.7703 (m) cc_final: 0.7483 (t) REVERT: A 152 THR cc_start: 0.7761 (m) cc_final: 0.7085 (p) REVERT: A 155 SER cc_start: 0.8702 (m) cc_final: 0.8502 (m) REVERT: A 156 VAL cc_start: 0.7984 (t) cc_final: 0.7716 (p) REVERT: A 167 MET cc_start: 0.6059 (mmm) cc_final: 0.5748 (ptp) REVERT: A 301 ILE cc_start: 0.7711 (mt) cc_final: 0.7502 (mt) REVERT: A 366 THR cc_start: 0.8164 (p) cc_final: 0.7886 (p) REVERT: A 369 ILE cc_start: 0.7835 (tp) cc_final: 0.7619 (tp) REVERT: A 386 LEU cc_start: 0.8009 (mt) cc_final: 0.7794 (mm) REVERT: A 423 VAL cc_start: 0.7654 (t) cc_final: 0.7204 (m) outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.1260 time to fit residues: 14.7382 Evaluate side-chains 89 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3246 Z= 0.265 Angle : 0.647 5.754 4437 Z= 0.343 Chirality : 0.043 0.157 502 Planarity : 0.005 0.043 529 Dihedral : 13.939 158.406 440 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.40 % Allowed : 13.81 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.42), residues: 384 helix: 0.94 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -2.82 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 12 HIS 0.003 0.001 HIS A 364 PHE 0.019 0.002 PHE A 439 TYR 0.029 0.002 TYR A 445 ARG 0.002 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7917 (mmm) cc_final: 0.7416 (mpp) REVERT: A 128 TYR cc_start: 0.6859 (m-80) cc_final: 0.6476 (m-80) REVERT: A 152 THR cc_start: 0.8032 (m) cc_final: 0.7314 (p) REVERT: A 156 VAL cc_start: 0.7986 (t) cc_final: 0.7726 (p) REVERT: A 298 TYR cc_start: 0.7251 (m-10) cc_final: 0.6576 (m-10) REVERT: A 363 MET cc_start: 0.6517 (tpt) cc_final: 0.6156 (mtt) REVERT: A 364 HIS cc_start: 0.6641 (t-90) cc_final: 0.6389 (t-90) REVERT: A 423 VAL cc_start: 0.7872 (t) cc_final: 0.7435 (m) REVERT: A 440 LEU cc_start: 0.7236 (tp) cc_final: 0.6626 (mt) outliers start: 8 outliers final: 3 residues processed: 102 average time/residue: 0.1167 time to fit residues: 15.0800 Evaluate side-chains 93 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3246 Z= 0.185 Angle : 0.633 6.564 4437 Z= 0.324 Chirality : 0.041 0.151 502 Planarity : 0.005 0.066 529 Dihedral : 13.860 157.996 440 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.40 % Allowed : 18.32 % Favored : 79.28 % 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: 0.57 (0.42), residues: 384 helix: 1.22 (0.29), residues: 295 sheet: None (None), residues: 0 loop : -2.53 (0.64), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.013 0.001 PHE A 439 TYR 0.028 0.002 TYR A 126 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7923 (mmm) cc_final: 0.7609 (mmm) REVERT: A 152 THR cc_start: 0.7897 (m) cc_final: 0.7244 (p) REVERT: A 156 VAL cc_start: 0.7953 (t) cc_final: 0.7661 (p) REVERT: A 366 THR cc_start: 0.8228 (p) cc_final: 0.8000 (p) REVERT: A 423 VAL cc_start: 0.7850 (t) cc_final: 0.7431 (m) outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.1072 time to fit residues: 13.2192 Evaluate side-chains 94 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3246 Z= 0.256 Angle : 0.686 6.367 4437 Z= 0.353 Chirality : 0.042 0.144 502 Planarity : 0.005 0.059 529 Dihedral : 13.567 157.946 440 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.90 % Allowed : 17.42 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.42), residues: 384 helix: 1.24 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -2.37 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 94 HIS 0.005 0.001 HIS A 364 PHE 0.016 0.002 PHE A 266 TYR 0.024 0.002 TYR A 376 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8035 (mmm) cc_final: 0.7586 (mmm) REVERT: A 128 TYR cc_start: 0.6977 (m-80) cc_final: 0.6579 (m-80) REVERT: A 152 THR cc_start: 0.7904 (m) cc_final: 0.7362 (p) REVERT: A 167 MET cc_start: 0.6597 (mmm) cc_final: 0.6308 (ptp) REVERT: A 384 MET cc_start: 0.6875 (tpp) cc_final: 0.6534 (mpp) REVERT: A 386 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7283 (tt) REVERT: A 423 VAL cc_start: 0.7865 (t) cc_final: 0.7455 (m) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.1038 time to fit residues: 12.5401 Evaluate side-chains 95 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3246 Z= 0.220 Angle : 0.664 6.604 4437 Z= 0.338 Chirality : 0.041 0.135 502 Planarity : 0.004 0.054 529 Dihedral : 13.714 156.091 440 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.30 % Allowed : 19.22 % Favored : 77.48 % 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: 0.87 (0.43), residues: 384 helix: 1.31 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.12 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.009 0.002 HIS A 364 PHE 0.016 0.001 PHE A 266 TYR 0.023 0.002 TYR A 445 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8034 (mmm) cc_final: 0.7561 (mmm) REVERT: A 128 TYR cc_start: 0.6978 (m-80) cc_final: 0.6633 (m-80) REVERT: A 152 THR cc_start: 0.7908 (m) cc_final: 0.7247 (p) REVERT: A 156 VAL cc_start: 0.7967 (t) cc_final: 0.7720 (p) REVERT: A 167 MET cc_start: 0.6725 (mmm) cc_final: 0.6309 (ptp) REVERT: A 386 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7273 (tt) REVERT: A 391 VAL cc_start: 0.8531 (t) cc_final: 0.8293 (p) REVERT: A 423 VAL cc_start: 0.7855 (t) cc_final: 0.7433 (m) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.0920 time to fit residues: 11.3218 Evaluate side-chains 95 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3246 Z= 0.264 Angle : 0.699 6.851 4437 Z= 0.357 Chirality : 0.042 0.137 502 Planarity : 0.004 0.047 529 Dihedral : 13.851 160.262 440 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.30 % Allowed : 19.52 % Favored : 77.18 % 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: 0.78 (0.43), residues: 384 helix: 1.25 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.13 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.007 0.002 HIS A 364 PHE 0.017 0.002 PHE A 266 TYR 0.024 0.002 TYR A 376 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8068 (mmm) cc_final: 0.7619 (mmm) REVERT: A 128 TYR cc_start: 0.7043 (m-80) cc_final: 0.6742 (m-80) REVERT: A 152 THR cc_start: 0.7915 (m) cc_final: 0.7414 (p) REVERT: A 167 MET cc_start: 0.6475 (mmm) cc_final: 0.6013 (ptp) REVERT: A 298 TYR cc_start: 0.7021 (m-10) cc_final: 0.6702 (m-10) REVERT: A 386 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7220 (tt) REVERT: A 391 VAL cc_start: 0.8550 (t) cc_final: 0.8344 (p) REVERT: A 423 VAL cc_start: 0.7887 (t) cc_final: 0.7470 (m) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.0915 time to fit residues: 11.1203 Evaluate side-chains 93 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.6387 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 3246 Z= 0.296 Angle : 0.720 6.870 4437 Z= 0.369 Chirality : 0.043 0.137 502 Planarity : 0.004 0.045 529 Dihedral : 13.874 159.083 440 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.30 % Allowed : 20.72 % Favored : 75.98 % 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: 0.68 (0.43), residues: 384 helix: 1.14 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -2.05 (0.69), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.007 0.002 HIS A 364 PHE 0.022 0.002 PHE A 266 TYR 0.028 0.002 TYR A 376 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8077 (mmm) cc_final: 0.7632 (mmm) REVERT: A 128 TYR cc_start: 0.7097 (m-80) cc_final: 0.6789 (m-80) REVERT: A 152 THR cc_start: 0.8051 (m) cc_final: 0.7534 (p) REVERT: A 298 TYR cc_start: 0.7013 (m-10) cc_final: 0.6674 (m-10) REVERT: A 386 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7195 (tt) REVERT: A 391 VAL cc_start: 0.8523 (t) cc_final: 0.8314 (p) REVERT: A 423 VAL cc_start: 0.7904 (t) cc_final: 0.7489 (m) REVERT: A 445 TYR cc_start: 0.6615 (t80) cc_final: 0.6408 (t80) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.0985 time to fit residues: 11.7753 Evaluate side-chains 95 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3246 Z= 0.231 Angle : 0.703 9.208 4437 Z= 0.350 Chirality : 0.041 0.130 502 Planarity : 0.004 0.038 529 Dihedral : 13.989 168.568 440 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.70 % Allowed : 21.32 % Favored : 75.98 % 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: 1.01 (0.43), residues: 384 helix: 1.38 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -1.93 (0.71), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.014 0.002 PHE A 266 TYR 0.027 0.002 TYR A 126 ARG 0.001 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8072 (mmm) cc_final: 0.7658 (mmm) REVERT: A 128 TYR cc_start: 0.7093 (m-80) cc_final: 0.6751 (m-80) REVERT: A 152 THR cc_start: 0.8053 (m) cc_final: 0.7555 (p) REVERT: A 298 TYR cc_start: 0.6858 (m-10) cc_final: 0.6625 (m-10) REVERT: A 386 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7105 (tt) REVERT: A 423 VAL cc_start: 0.7890 (t) cc_final: 0.7481 (m) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.1064 time to fit residues: 12.9269 Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3246 Z= 0.253 Angle : 0.723 9.357 4437 Z= 0.363 Chirality : 0.042 0.133 502 Planarity : 0.004 0.033 529 Dihedral : 13.860 165.327 440 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.30 % Allowed : 21.92 % Favored : 74.77 % 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: 0.98 (0.43), residues: 384 helix: 1.34 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -1.90 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.017 0.002 PHE A 266 TYR 0.028 0.002 TYR A 126 ARG 0.002 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8081 (mmm) cc_final: 0.7685 (mmm) REVERT: A 128 TYR cc_start: 0.7109 (m-80) cc_final: 0.6770 (m-80) REVERT: A 152 THR cc_start: 0.8071 (m) cc_final: 0.7562 (p) REVERT: A 298 TYR cc_start: 0.6901 (m-10) cc_final: 0.6672 (m-10) REVERT: A 386 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7099 (tt) REVERT: A 423 VAL cc_start: 0.7897 (t) cc_final: 0.7491 (m) REVERT: A 445 TYR cc_start: 0.6550 (t80) cc_final: 0.6179 (t80) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.0963 time to fit residues: 11.9015 Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140362 restraints weight = 5380.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.144524 restraints weight = 2934.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147309 restraints weight = 1807.006| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3246 Z= 0.244 Angle : 0.713 9.229 4437 Z= 0.357 Chirality : 0.041 0.133 502 Planarity : 0.004 0.029 529 Dihedral : 13.729 163.137 440 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.30 % Allowed : 21.92 % Favored : 74.77 % 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: 1.04 (0.43), residues: 384 helix: 1.36 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -1.81 (0.73), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.016 0.002 PHE A 266 TYR 0.027 0.002 TYR A 126 ARG 0.002 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1120.76 seconds wall clock time: 20 minutes 36.13 seconds (1236.13 seconds total)