Starting phenix.real_space_refine on Thu Feb 13 05:38:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgx_37520/02_2025/8wgx_37520_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgx_37520/02_2025/8wgx_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/cci-nas-00/data/ceres_data/8wgx_37520/02_2025/8wgx_37520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgx_37520/02_2025/8wgx_37520.map" model { file = "/net/cci-nas-00/data/ceres_data/8wgx_37520/02_2025/8wgx_37520_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgx_37520/02_2025/8wgx_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. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.45, per 1000 atoms: 0.51 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 750.4 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: 0.75 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: 3.23 Time building geometry restraints manager: 2.74 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: 0.00 - 7.11: 16037 7.11 - 14.21: 0 14.21 - 21.32: 0 21.32 - 28.42: 0 28.42 - 35.53: 3 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: 0.550 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.604 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: 0.2518 time to fit residues: 23.4576 Evaluate side-chains 63 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.182431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155630 restraints weight = 15349.205| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.25 r_work: 0.3686 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.629 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: 0.8647 (OUTLIER) cc_final: 0.7628 (t80) REVERT: A 245 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7700 (t) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.2911 time to fit residues: 30.1256 Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158788 restraints weight = 15461.492| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.22 r_work: 0.3725 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1216 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= 0.181 Angle : 0.492 5.124 6190 Z= 0.265 Chirality : 0.039 0.375 691 Planarity : 0.004 0.037 751 Dihedral : 5.096 55.882 602 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 21.04 % 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: 1.20 (0.36), residues: 543 helix: 1.21 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.14 (0.53), residues: 149 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 81 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.669 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: 0.8741 (OUTLIER) cc_final: 0.7435 (t80) REVERT: A 245 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7681 (t) REVERT: A 313 THR cc_start: 0.8924 (t) cc_final: 0.8493 (p) REVERT: A 352 ILE cc_start: 0.7839 (mm) cc_final: 0.7550 (mt) REVERT: A 395 ILE cc_start: 0.8434 (mt) cc_final: 0.8113 (mt) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.2897 time to fit residues: 30.1888 Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158923 restraints weight = 15213.890| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.20 r_work: 0.3724 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1463 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 : 0.487 5.012 6190 Z= 0.262 Chirality : 0.039 0.377 691 Planarity : 0.004 0.037 751 Dihedral : 4.895 53.014 602 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: 1.38 (0.37), residues: 543 helix: 1.35 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.05 (0.54), 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 228 PHE 0.011 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 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 77 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.683 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: 0.8819 (OUTLIER) cc_final: 0.7335 (t80) REVERT: A 245 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7781 (t) REVERT: A 313 THR cc_start: 0.9023 (t) cc_final: 0.8623 (p) REVERT: A 352 ILE cc_start: 0.7909 (mm) cc_final: 0.7650 (mt) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.2968 time to fit residues: 29.5325 Evaluate side-chains 75 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.179776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153272 restraints weight = 15445.424| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.23 r_work: 0.3660 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4538 Z= 0.308 Angle : 0.553 5.474 6190 Z= 0.302 Chirality : 0.041 0.377 691 Planarity : 0.004 0.035 751 Dihedral : 5.406 49.949 602 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.82 % Allowed : 21.48 % 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: 1.10 (0.36), residues: 543 helix: 1.13 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.13 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.004 0.001 HIS A 228 PHE 0.016 0.002 PHE A 207 TYR 0.021 0.002 TYR A 84 ARG 0.001 0.000 ARG A 301 *********************** 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 85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.634 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: 0.8815 (m-10) cc_final: 0.8558 (m-10) REVERT: A 229 ASP cc_start: 0.7728 (t0) cc_final: 0.7479 (t0) REVERT: A 234 GLN cc_start: 0.7233 (tp40) cc_final: 0.7025 (tp40) REVERT: A 245 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (t) REVERT: A 303 LYS cc_start: 0.7727 (mtpt) cc_final: 0.6999 (tptm) REVERT: A 352 ILE cc_start: 0.7934 (mm) cc_final: 0.7666 (mt) REVERT: A 518 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7901 (mtm180) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.2834 time to fit residues: 29.9833 Evaluate side-chains 75 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 ILE 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 27 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159270 restraints weight = 15209.311| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.19 r_work: 0.3728 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4538 Z= 0.150 Angle : 0.470 4.796 6190 Z= 0.253 Chirality : 0.039 0.377 691 Planarity : 0.004 0.037 751 Dihedral : 4.368 27.635 600 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 23.21 % Favored : 75.05 % 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: 1.46 (0.37), residues: 543 helix: 1.39 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -0.00 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.001 0.000 ARG A 442 *********************** 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 75 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7762 (t0) cc_final: 0.7341 (t0) REVERT: A 245 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 300 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6841 (p90) REVERT: A 303 LYS cc_start: 0.7763 (mtpt) cc_final: 0.6972 (tptm) REVERT: A 313 THR cc_start: 0.9003 (t) cc_final: 0.8597 (p) REVERT: A 352 ILE cc_start: 0.7841 (mm) cc_final: 0.7598 (mt) REVERT: A 518 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7959 (mtp85) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.2687 time to fit residues: 26.5139 Evaluate side-chains 68 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 300 TYR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE 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 53 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.183952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157726 restraints weight = 15360.160| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.25 r_work: 0.3709 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2091 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= 0.195 Angle : 0.485 4.958 6190 Z= 0.261 Chirality : 0.039 0.378 691 Planarity : 0.004 0.037 751 Dihedral : 4.423 26.848 600 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.17 % Allowed : 22.99 % Favored : 74.84 % 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: 1.50 (0.37), residues: 543 helix: 1.47 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.05 (0.52), residues: 157 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 0.001 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 72 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7551 (t0) cc_final: 0.7210 (t0) REVERT: A 245 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7668 (t) REVERT: A 303 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7025 (tptm) REVERT: A 313 THR cc_start: 0.8947 (t) cc_final: 0.8540 (p) REVERT: A 352 ILE cc_start: 0.7881 (mm) cc_final: 0.7640 (mt) REVERT: A 518 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7672 (mtm180) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2605 time to fit residues: 25.2713 Evaluate side-chains 68 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain A residue 564 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156435 restraints weight = 15578.991| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.27 r_work: 0.3695 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4538 Z= 0.209 Angle : 0.492 4.948 6190 Z= 0.265 Chirality : 0.039 0.379 691 Planarity : 0.004 0.038 751 Dihedral : 4.453 27.032 600 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.95 % Allowed : 22.99 % Favored : 75.05 % 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: 1.52 (0.37), residues: 543 helix: 1.47 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.02 (0.52), residues: 157 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 0.001 0.000 ARG A 587 *********************** 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 75 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7689 (t0) cc_final: 0.7328 (t0) REVERT: A 245 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7639 (t) REVERT: A 303 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7047 (tptm) REVERT: A 313 THR cc_start: 0.8956 (t) cc_final: 0.8547 (p) REVERT: A 352 ILE cc_start: 0.7963 (mm) cc_final: 0.7716 (mt) REVERT: A 518 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7741 (mtm180) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.3459 time to fit residues: 32.2810 Evaluate side-chains 72 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 564 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156440 restraints weight = 15512.591| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.26 r_work: 0.3692 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4538 Z= 0.209 Angle : 0.494 4.907 6190 Z= 0.266 Chirality : 0.039 0.379 691 Planarity : 0.004 0.038 751 Dihedral : 4.488 27.352 600 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.17 % Allowed : 22.34 % 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: 1.52 (0.37), residues: 543 helix: 1.42 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 0.08 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.001 0.000 ARG A 587 *********************** 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 77 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7776 (t0) cc_final: 0.7380 (t0) REVERT: A 245 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7650 (t) REVERT: A 303 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7084 (tptm) REVERT: A 313 THR cc_start: 0.8956 (t) cc_final: 0.8551 (p) REVERT: A 352 ILE cc_start: 0.7964 (mm) cc_final: 0.7715 (mt) REVERT: A 518 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7728 (mtm180) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.3575 time to fit residues: 34.2885 Evaluate side-chains 75 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 315 ILE 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 Chi-restraints excluded: chain A residue 564 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.183741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157575 restraints weight = 15399.752| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.23 r_work: 0.3711 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2443 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= 0.185 Angle : 0.483 4.799 6190 Z= 0.259 Chirality : 0.039 0.378 691 Planarity : 0.004 0.038 751 Dihedral : 4.380 26.786 600 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 1.65 (0.37), residues: 543 helix: 1.56 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.07 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 220 PHE 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.002 0.000 ARG A 607 ********************** 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 79 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7987 (t0) cc_final: 0.7601 (t0) REVERT: A 245 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7807 (t) REVERT: A 303 LYS cc_start: 0.7677 (mtpt) cc_final: 0.7042 (tptm) REVERT: A 313 THR cc_start: 0.9007 (t) cc_final: 0.8619 (p) REVERT: A 352 ILE cc_start: 0.7985 (mm) cc_final: 0.7744 (mt) REVERT: A 518 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7771 (mtm180) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.3806 time to fit residues: 36.6689 Evaluate side-chains 76 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 315 ILE 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 Chi-restraints excluded: chain A residue 564 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.185681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159573 restraints weight = 15330.549| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.23 r_work: 0.3729 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4538 Z= 0.157 Angle : 0.467 4.677 6190 Z= 0.250 Chirality : 0.039 0.378 691 Planarity : 0.004 0.038 751 Dihedral : 4.173 25.408 600 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 1.85 (0.37), residues: 543 helix: 1.66 (0.27), residues: 389 sheet: None (None), residues: 0 loop : 0.27 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.009 0.001 PHE A 362 TYR 0.019 0.001 TYR A 151 ARG 0.003 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4388.56 seconds wall clock time: 77 minutes 39.75 seconds (4659.75 seconds total)