Starting phenix.real_space_refine on Sat Aug 3 18:34:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgx_37520/08_2024/8wgx_37520_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgx_37520/08_2024/8wgx_37520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgx_37520/08_2024/8wgx_37520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgx_37520/08_2024/8wgx_37520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgx_37520/08_2024/8wgx_37520_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgx_37520/08_2024/8wgx_37520_trim.cif" } resolution = 3.47 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= 0.006 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 2953 2.51 5 N 681 2.21 5 O 743 1.98 5 H 4363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 8736 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LNR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.90, per 1000 atoms: 0.56 Number of scatterers: 8760 At special positions: 0 Unit cell: (73.61, 70.3625, 100.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 743 8.00 N 681 7.00 C 2953 6.00 H 4363 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.16 Conformation dependent library (CDL) restraints added in 964.6 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 84.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.729A pdb=" N ALA A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.647A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 105 Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.528A pdb=" N ARG A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.523A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.965A pdb=" N LYS A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.757A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.629A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.655A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.072A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.904A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.593A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.579A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.844A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.578A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.703A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.769A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 301 hydrogen bonds defined for protein. 861 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: 3.55 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4356 1.03 - 1.23: 12 1.23 - 1.42: 2014 1.42 - 1.62: 2488 1.62 - 1.82: 31 Bond restraints: 8901 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.19e+00 bond pdb=" C TYR A 147 " pdb=" O TYR A 147 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.52e+00 bond pdb=" CA ALA A 305 " pdb=" CB ALA A 305 " ideal model delta sigma weight residual 1.541 1.529 0.012 1.20e-02 6.94e+03 9.35e-01 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.525 1.512 0.013 1.37e-02 5.33e+03 9.11e-01 bond pdb=" N GLY A 478 " pdb=" CA GLY A 478 " ideal model delta sigma weight residual 1.460 1.448 0.012 1.26e-02 6.30e+03 8.96e-01 ... (remaining 8896 not shown) Histogram of bond angle deviations from ideal: 73.47 - 85.57: 3 85.57 - 97.68: 0 97.68 - 109.78: 6308 109.78 - 121.88: 8289 121.88 - 133.99: 1440 Bond angle restraints: 16040 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 73.47 35.53 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 75.75 34.25 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 76.16 32.84 3.00e+00 1.11e-01 1.20e+02 angle pdb=" N ALA A 305 " pdb=" CA ALA A 305 " pdb=" CB ALA A 305 " ideal model delta sigma weight residual 114.17 110.19 3.98 1.14e+00 7.69e-01 1.22e+01 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 118.51 -4.61 1.80e+00 3.09e-01 6.55e+00 ... (remaining 16035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3731 18.02 - 36.05: 334 36.05 - 54.07: 120 54.07 - 72.09: 29 72.09 - 90.11: 2 Dihedral angle restraints: 4216 sinusoidal: 2141 harmonic: 2075 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -131.79 9.19 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 131.31 -8.51 0 2.50e+00 1.60e-01 1.16e+01 ... (remaining 4213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 648 0.077 - 0.153: 41 0.153 - 0.230: 1 0.230 - 0.306: 0 0.306 - 0.382: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CAL LNR A 702 " pdb=" CAH LNR A 702 " pdb=" CAK LNR A 702 " pdb=" OAD LNR A 702 " both_signs ideal model delta sigma weight residual False -2.28 -2.44 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CAL LNR A 701 " pdb=" CAH LNR A 701 " pdb=" CAK LNR A 701 " pdb=" OAD LNR A 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.43 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 688 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE A 103 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C VAL A 492 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C LEU A 102 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.011 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 571 2.21 - 2.80: 17655 2.80 - 3.40: 24644 3.40 - 4.00: 31341 4.00 - 4.60: 49344 Nonbonded interactions: 123555 Sorted by model distance: nonbonded pdb=" H TYR A 205 " pdb=" HA TYR A 205 " model vdw 1.607 1.816 nonbonded pdb="HD22 ASN A 78 " pdb=" OD1 ASN A 350 " model vdw 1.615 2.450 nonbonded pdb=" O GLY A 91 " pdb=" H PHE A 94 " model vdw 1.640 2.450 nonbonded pdb=" HH TYR A 139 " pdb=" OD2 ASP A 434 " model vdw 1.676 2.450 nonbonded pdb=" OE2 GLU A 122 " pdb=" HZ3 LYS A 129 " model vdw 1.679 2.450 ... (remaining 123550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.130 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 34.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.003 0.040 4538 Z= 0.188 Angle : 0.542 4.606 6190 Z= 0.301 Chirality : 0.041 0.382 691 Planarity : 0.004 0.035 751 Dihedral : 16.221 90.114 1528 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.22 % Allowed : 21.04 % Favored : 78.74 % 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: 1.83 (0.37), residues: 543 helix: 1.61 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.46 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 228 PHE 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (t80) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2471 time to fit residues: 22.9628 Evaluate side-chains 63 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4538 Z= 0.295 Angle : 0.555 5.257 6190 Z= 0.302 Chirality : 0.041 0.379 691 Planarity : 0.004 0.035 751 Dihedral : 5.711 58.105 602 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.17 % Allowed : 20.39 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.36), residues: 543 helix: 1.17 (0.26), residues: 389 sheet: None (None), residues: 0 loop : 0.02 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS A 599 PHE 0.015 0.001 PHE A 362 TYR 0.021 0.002 TYR A 84 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7553 (t80) REVERT: A 245 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7695 (t) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.2908 time to fit residues: 30.0140 Evaluate side-chains 74 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 39 optimal weight: 0.1980 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 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4538 Z= 0.150 Angle : 0.477 5.087 6190 Z= 0.255 Chirality : 0.038 0.374 691 Planarity : 0.004 0.038 751 Dihedral : 5.020 56.602 602 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.74 % Allowed : 20.61 % Favored : 77.66 % 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: 1.36 (0.37), residues: 543 helix: 1.32 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.01 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 228 PHE 0.010 0.001 PHE A 110 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 313 THR cc_start: 0.8895 (t) cc_final: 0.8435 (p) REVERT: A 352 ILE cc_start: 0.7866 (mm) cc_final: 0.7562 (mt) REVERT: A 395 ILE cc_start: 0.8439 (mt) cc_final: 0.8158 (mt) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.2767 time to fit residues: 28.3732 Evaluate side-chains 73 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.0370 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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: 0.7326 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4538 Z= 0.193 Angle : 0.486 5.076 6190 Z= 0.261 Chirality : 0.039 0.376 691 Planarity : 0.004 0.037 751 Dihedral : 4.886 53.859 602 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.74 % Allowed : 20.39 % Favored : 77.87 % 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: 1.41 (0.37), residues: 543 helix: 1.36 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.02 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 PHE 0.011 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7205 (t80) REVERT: A 245 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7594 (t) REVERT: A 313 THR cc_start: 0.8920 (t) cc_final: 0.8464 (p) REVERT: A 352 ILE cc_start: 0.7915 (mm) cc_final: 0.7634 (mt) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.2846 time to fit residues: 28.4295 Evaluate side-chains 77 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7385 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4538 Z= 0.252 Angle : 0.520 5.222 6190 Z= 0.283 Chirality : 0.040 0.377 691 Planarity : 0.004 0.036 751 Dihedral : 5.185 50.545 602 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.39 % Allowed : 20.61 % Favored : 77.01 % 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: 1.24 (0.36), residues: 543 helix: 1.25 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.12 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.004 0.001 HIS A 228 PHE 0.016 0.002 PHE A 207 TYR 0.020 0.002 TYR A 151 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8481 (m-10) cc_final: 0.8263 (m-10) REVERT: A 245 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7682 (t) REVERT: A 303 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7220 (tptm) REVERT: A 352 ILE cc_start: 0.7938 (mm) cc_final: 0.7672 (mt) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.2820 time to fit residues: 29.9508 Evaluate side-chains 77 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4538 Z= 0.169 Angle : 0.476 4.810 6190 Z= 0.256 Chirality : 0.039 0.377 691 Planarity : 0.004 0.038 751 Dihedral : 4.404 26.949 600 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 22.56 % Favored : 75.70 % 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: 1.45 (0.37), residues: 543 helix: 1.40 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -0.06 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 PHE 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8460 (m-10) cc_final: 0.8231 (m-10) REVERT: A 245 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7635 (t) REVERT: A 303 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7210 (tptm) REVERT: A 313 THR cc_start: 0.8947 (t) cc_final: 0.8514 (p) REVERT: A 352 ILE cc_start: 0.7943 (mm) cc_final: 0.7679 (mt) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.2395 time to fit residues: 24.1220 Evaluate side-chains 69 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4538 Z= 0.159 Angle : 0.469 4.813 6190 Z= 0.252 Chirality : 0.039 0.376 691 Planarity : 0.004 0.038 751 Dihedral : 4.226 25.287 600 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.74 % Allowed : 22.34 % Favored : 75.92 % 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: 1.62 (0.37), residues: 543 helix: 1.51 (0.27), residues: 394 sheet: None (None), residues: 0 loop : 0.07 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.003 0.000 HIS A 228 PHE 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7603 (t) REVERT: A 303 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7193 (tptm) REVERT: A 313 THR cc_start: 0.8921 (t) cc_final: 0.8466 (p) REVERT: A 352 ILE cc_start: 0.7921 (mm) cc_final: 0.7662 (mt) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.2402 time to fit residues: 22.8417 Evaluate side-chains 69 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7336 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4538 Z= 0.178 Angle : 0.474 4.825 6190 Z= 0.255 Chirality : 0.039 0.377 691 Planarity : 0.004 0.039 751 Dihedral : 4.257 25.095 600 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 22.13 % Favored : 75.70 % 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: 1.71 (0.37), residues: 543 helix: 1.62 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.03 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.004 0.001 HIS A 228 PHE 0.011 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7490 (t) REVERT: A 303 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7187 (tptm) REVERT: A 313 THR cc_start: 0.8929 (t) cc_final: 0.8470 (p) REVERT: A 352 ILE cc_start: 0.7920 (mm) cc_final: 0.7650 (mt) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.2752 time to fit residues: 27.5803 Evaluate side-chains 70 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4538 Z= 0.168 Angle : 0.476 4.749 6190 Z= 0.255 Chirality : 0.039 0.377 691 Planarity : 0.004 0.039 751 Dihedral : 4.205 25.035 600 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.52 % Allowed : 23.21 % Favored : 75.27 % 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: 543 helix: 1.62 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.07 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.003 0.000 HIS A 228 PHE 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7481 (t) REVERT: A 303 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7185 (tptm) REVERT: A 313 THR cc_start: 0.8937 (t) cc_final: 0.8481 (p) REVERT: A 352 ILE cc_start: 0.7984 (mm) cc_final: 0.7719 (mt) outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.2459 time to fit residues: 23.8536 Evaluate side-chains 70 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4538 Z= 0.175 Angle : 0.477 4.768 6190 Z= 0.256 Chirality : 0.039 0.378 691 Planarity : 0.004 0.039 751 Dihedral : 4.234 25.176 600 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.52 % Allowed : 22.99 % Favored : 75.49 % 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: 1.66 (0.37), residues: 543 helix: 1.55 (0.27), residues: 394 sheet: None (None), residues: 0 loop : 0.02 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 228 PHE 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 303 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7196 (tptm) REVERT: A 313 THR cc_start: 0.8932 (t) cc_final: 0.8481 (p) REVERT: A 352 ILE cc_start: 0.7983 (mm) cc_final: 0.7713 (mt) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.3142 time to fit residues: 30.6520 Evaluate side-chains 75 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.156125 restraints weight = 14842.593| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.01 r_work: 0.3731 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4538 Z= 0.192 Angle : 0.490 4.809 6190 Z= 0.263 Chirality : 0.039 0.379 691 Planarity : 0.004 0.039 751 Dihedral : 4.328 25.667 600 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 22.56 % Favored : 75.27 % 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: 1.64 (0.37), residues: 543 helix: 1.54 (0.27), residues: 392 sheet: None (None), residues: 0 loop : 0.01 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 441 PHE 0.011 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.15 seconds wall clock time: 45 minutes 54.70 seconds (2754.70 seconds total)