Starting phenix.real_space_refine on Sat Jun 7 11:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgx_37520/06_2025/8wgx_37520_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgx_37520/06_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_37520/06_2025/8wgx_37520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgx_37520/06_2025/8wgx_37520.map" model { file = "/net/cci-nas-00/data/ceres_data/8wgx_37520/06_2025/8wgx_37520_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgx_37520/06_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.67, per 1000 atoms: 0.53 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: 2.44 Conformation dependent library (CDL) restraints added in 719.8 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: 0.71 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: 2.97 Time building geometry restraints manager: 2.90 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: 0.440 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.940 Find NCS groups from input model: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- 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 4539 Z= 0.146 Angle : 0.543 4.606 6192 Z= 0.302 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 Details of bonding type rmsd hydrogen bonds : bond 0.12295 ( 301) hydrogen bonds : angle 5.08096 ( 861) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.91887 ( 2) covalent geometry : bond 0.00302 ( 4538) covalent geometry : angle 0.54247 ( 6190) *********************** 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 : 0.685 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: 0.2340 time to fit residues: 21.9620 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 : 0.620 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155631 restraints weight = 15349.215| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.24 r_work: 0.3687 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 4539 Z= 0.199 Angle : 0.555 5.257 6192 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 Details of bonding type rmsd hydrogen bonds : bond 0.05327 ( 301) hydrogen bonds : angle 4.86332 ( 861) SS BOND : bond 0.00280 ( 1) SS BOND : angle 1.10860 ( 2) covalent geometry : bond 0.00466 ( 4538) covalent geometry : angle 0.55495 ( 6190) *********************** 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 : 0.609 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: 0.8715 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 245 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7802 (t) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.2799 time to fit residues: 29.1644 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 : 0.607 ------------------------------------------------------------------------------- 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: 0.4980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 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 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158903 restraints weight = 15447.138| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.22 r_work: 0.3727 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4539 Z= 0.129 Angle : 0.491 5.110 6192 Z= 0.264 Chirality : 0.039 0.376 691 Planarity : 0.004 0.037 751 Dihedral : 5.111 56.024 602 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 20.17 % 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: 1.19 (0.36), residues: 543 helix: 1.21 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.13 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 301) hydrogen bonds : angle 4.66071 ( 861) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.94311 ( 2) covalent geometry : bond 0.00287 ( 4538) covalent geometry : angle 0.49074 ( 6190) *********************** 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 : 0.650 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: 0.8798 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 245 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7791 (t) REVERT: A 313 THR cc_start: 0.8980 (t) cc_final: 0.8568 (p) REVERT: A 352 ILE cc_start: 0.7880 (mm) cc_final: 0.7606 (mt) REVERT: A 395 ILE cc_start: 0.8518 (mt) cc_final: 0.8174 (mt) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.2780 time to fit residues: 29.1292 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 : 0.632 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.185356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159278 restraints weight = 15187.515| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.19 r_work: 0.3730 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4539 Z= 0.131 Angle : 0.483 5.032 6192 Z= 0.260 Chirality : 0.039 0.377 691 Planarity : 0.004 0.037 751 Dihedral : 4.859 53.516 602 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.74 % Allowed : 21.04 % Favored : 77.22 % 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: 1.40 (0.37), residues: 543 helix: 1.34 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.01 (0.54), 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 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 301) hydrogen bonds : angle 4.57364 ( 861) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.87559 ( 2) covalent geometry : bond 0.00297 ( 4538) covalent geometry : angle 0.48312 ( 6190) *********************** 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 : 0.634 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: 0.8805 (OUTLIER) cc_final: 0.7287 (t80) REVERT: A 245 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7765 (t) REVERT: A 313 THR cc_start: 0.9016 (t) cc_final: 0.8614 (p) REVERT: A 352 ILE cc_start: 0.7894 (mm) cc_final: 0.7640 (mt) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.2686 time to fit residues: 26.5788 Evaluate side-chains 73 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.180343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153828 restraints weight = 15425.082| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.24 r_work: 0.3666 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4539 Z= 0.196 Angle : 0.545 5.327 6192 Z= 0.298 Chirality : 0.041 0.379 691 Planarity : 0.004 0.035 751 Dihedral : 5.345 50.296 602 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.60 % Allowed : 20.82 % Favored : 76.57 % 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: 1.14 (0.36), residues: 543 helix: 1.16 (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 0.012 0.001 TRP A 80 HIS 0.005 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 587 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 301) hydrogen bonds : angle 4.82876 ( 861) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.95803 ( 2) covalent geometry : bond 0.00460 ( 4538) covalent geometry : angle 0.54433 ( 6190) *********************** 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: 12 poor density : 73 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: A 207 PHE cc_start: 0.8802 (m-10) cc_final: 0.8530 (m-10) REVERT: A 229 ASP cc_start: 0.7738 (t0) cc_final: 0.7531 (t0) REVERT: A 234 GLN cc_start: 0.7228 (tp40) cc_final: 0.7014 (tp40) REVERT: A 245 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7809 (t) REVERT: A 303 LYS cc_start: 0.7712 (mtpt) cc_final: 0.6986 (tptm) REVERT: A 352 ILE cc_start: 0.8004 (mm) cc_final: 0.7751 (mt) REVERT: A 518 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7939 (mtm180) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.2931 time to fit residues: 31.5339 Evaluate side-chains 76 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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: 0.0040 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.184603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158667 restraints weight = 15242.214| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.19 r_work: 0.3720 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4539 Z= 0.117 Angle : 0.475 4.817 6192 Z= 0.255 Chirality : 0.039 0.376 691 Planarity : 0.004 0.037 751 Dihedral : 4.417 27.171 600 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.95 % Allowed : 22.78 % 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: 1.44 (0.37), residues: 543 helix: 1.39 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.06 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.001 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 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 301) hydrogen bonds : angle 4.57140 ( 861) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.90718 ( 2) covalent geometry : bond 0.00257 ( 4538) covalent geometry : angle 0.47485 ( 6190) *********************** 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: 9 poor density : 66 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7782 (t0) cc_final: 0.7345 (t0) REVERT: A 245 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7822 (t) REVERT: A 300 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6837 (p90) REVERT: A 303 LYS cc_start: 0.7788 (mtpt) cc_final: 0.6995 (tptm) REVERT: A 313 THR cc_start: 0.9015 (t) cc_final: 0.8629 (p) REVERT: A 352 ILE cc_start: 0.7848 (mm) cc_final: 0.7604 (mt) REVERT: A 518 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7981 (mtp85) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.3087 time to fit residues: 30.4661 Evaluate side-chains 69 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.183109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156916 restraints weight = 15382.198| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.23 r_work: 0.3705 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4539 Z= 0.146 Angle : 0.494 5.012 6192 Z= 0.267 Chirality : 0.039 0.378 691 Planarity : 0.004 0.037 751 Dihedral : 4.507 27.425 600 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: 1.47 (0.36), residues: 543 helix: 1.45 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.002 0.001 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 587 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 301) hydrogen bonds : angle 4.60890 ( 861) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.88353 ( 2) covalent geometry : bond 0.00337 ( 4538) covalent geometry : angle 0.49424 ( 6190) *********************** 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 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 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: 0.7894 (t0) cc_final: 0.7561 (t0) REVERT: A 245 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 303 LYS cc_start: 0.7709 (mtpt) cc_final: 0.6987 (tptm) REVERT: A 313 THR cc_start: 0.9004 (t) cc_final: 0.8620 (p) REVERT: A 352 ILE cc_start: 0.7935 (mm) cc_final: 0.7708 (mt) REVERT: A 518 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7992 (mtp85) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.3082 time to fit residues: 30.2247 Evaluate side-chains 71 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.182371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155852 restraints weight = 15563.912| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.27 r_work: 0.3684 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4539 Z= 0.151 Angle : 0.498 4.973 6192 Z= 0.269 Chirality : 0.039 0.379 691 Planarity : 0.004 0.037 751 Dihedral : 4.528 27.493 600 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.95 % Allowed : 22.78 % 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: 1.44 (0.37), residues: 543 helix: 1.38 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 0.02 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 301) hydrogen bonds : angle 4.63457 ( 861) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.82950 ( 2) covalent geometry : bond 0.00347 ( 4538) covalent geometry : angle 0.49811 ( 6190) *********************** 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 to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.658 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: 0.7980 (t0) cc_final: 0.7620 (t0) REVERT: A 245 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7775 (t) REVERT: A 303 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7012 (tptm) REVERT: A 313 THR cc_start: 0.9004 (t) cc_final: 0.8622 (p) REVERT: A 352 ILE cc_start: 0.7995 (mm) cc_final: 0.7756 (mt) REVERT: A 412 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7466 (mt) REVERT: A 518 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7849 (mtm180) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.3514 time to fit residues: 33.4373 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 : 0.696 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 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 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157103 restraints weight = 15476.222| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.26 r_work: 0.3701 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4539 Z= 0.133 Angle : 0.482 4.841 6192 Z= 0.259 Chirality : 0.039 0.378 691 Planarity : 0.004 0.038 751 Dihedral : 4.392 26.979 600 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 1.64 (0.37), residues: 543 helix: 1.54 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.09 (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 0.010 0.001 PHE A 362 TYR 0.020 0.001 TYR A 151 ARG 0.001 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 301) hydrogen bonds : angle 4.54922 ( 861) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.80114 ( 2) covalent geometry : bond 0.00303 ( 4538) covalent geometry : angle 0.48170 ( 6190) *********************** 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 78 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 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 229 ASP cc_start: 0.7768 (t0) cc_final: 0.7386 (t0) REVERT: A 245 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7680 (t) REVERT: A 303 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7077 (tptm) REVERT: A 313 THR cc_start: 0.8958 (t) cc_final: 0.8548 (p) REVERT: A 352 ILE cc_start: 0.7958 (mm) cc_final: 0.7708 (mt) REVERT: A 518 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7665 (mtm180) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.3542 time to fit residues: 34.3851 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 : 0.623 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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 = 0.183886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157678 restraints weight = 15392.541| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.24 r_work: 0.3710 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4539 Z= 0.130 Angle : 0.481 4.818 6192 Z= 0.259 Chirality : 0.039 0.378 691 Planarity : 0.004 0.038 751 Dihedral : 4.339 26.185 600 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.95 % Allowed : 22.56 % 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: 1.60 (0.37), residues: 543 helix: 1.50 (0.27), residues: 392 sheet: None (None), residues: 0 loop : 0.07 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 128 HIS 0.001 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 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 301) hydrogen bonds : angle 4.53318 ( 861) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.73709 ( 2) covalent geometry : bond 0.00295 ( 4538) covalent geometry : angle 0.48125 ( 6190) ********************** 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 80 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.075 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: 0.7963 (t0) cc_final: 0.7594 (t0) REVERT: A 245 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7794 (t) REVERT: A 303 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7020 (tptm) REVERT: A 313 THR cc_start: 0.9005 (t) cc_final: 0.8613 (p) REVERT: A 352 ILE cc_start: 0.7982 (mm) cc_final: 0.7739 (mt) REVERT: A 518 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7768 (mtm180) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.4373 time to fit residues: 44.4915 Evaluate side-chains 76 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.185841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159741 restraints weight = 15285.700| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.22 r_work: 0.3733 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4539 Z= 0.111 Angle : 0.468 4.656 6192 Z= 0.250 Chirality : 0.039 0.378 691 Planarity : 0.004 0.038 751 Dihedral : 4.163 25.075 600 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.74 % Allowed : 23.43 % 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: 1.82 (0.37), residues: 543 helix: 1.64 (0.27), residues: 391 sheet: None (None), residues: 0 loop : 0.23 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 128 HIS 0.001 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 607 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 301) hydrogen bonds : angle 4.44758 ( 861) SS BOND : bond 0.00160 ( 1) SS BOND : angle 0.72447 ( 2) covalent geometry : bond 0.00245 ( 4538) covalent geometry : angle 0.46749 ( 6190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5087.44 seconds wall clock time: 88 minutes 26.44 seconds (5306.44 seconds total)