Starting phenix.real_space_refine on Sat Aug 23 00:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgx_37520/08_2025/8wgx_37520_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgx_37520/08_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_37520/08_2025/8wgx_37520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgx_37520/08_2025/8wgx_37520.map" model { file = "/net/cci-nas-00/data/ceres_data/8wgx_37520/08_2025/8wgx_37520_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgx_37520/08_2025/8wgx_37520_trim.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.46, per 1000 atoms: 0.17 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: 0.49 Conformation dependent library (CDL) restraints added in 225.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.13 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: 1.57 Time building geometry restraints manager: 0.68 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: 0.460 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.870 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 518 TYR 0.020 0.001 TYR A 151 PHE 0.010 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4538) covalent geometry : angle 0.54247 ( 6190) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.91887 ( 2) hydrogen bonds : bond 0.12295 ( 301) hydrogen bonds : angle 5.08096 ( 861) *********************** 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 : 0.129 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: 0.8017 (t80) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.0816 time to fit residues: 7.8995 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 : 0.205 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.187921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161606 restraints weight = 15257.931| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.21 r_work: 0.3752 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4539 Z= 0.126 Angle : 0.493 5.016 6192 Z= 0.264 Chirality : 0.039 0.375 691 Planarity : 0.004 0.039 751 Dihedral : 5.404 58.365 602 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.30 % Allowed : 20.61 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.37), residues: 543 helix: 1.38 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.26 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.011 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4538) covalent geometry : angle 0.49286 ( 6190) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.95887 ( 2) hydrogen bonds : bond 0.04606 ( 301) hydrogen bonds : angle 4.61968 ( 861) *********************** 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 80 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.127 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: 0.8532 (OUTLIER) cc_final: 0.7829 (t80) REVERT: A 313 THR cc_start: 0.8884 (t) cc_final: 0.8461 (p) REVERT: A 352 ILE cc_start: 0.7844 (mm) cc_final: 0.7539 (mt) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.0988 time to fit residues: 10.1253 Evaluate side-chains 70 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 459 PHE Chi-restraints excluded: chain A residue 535 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.187670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161583 restraints weight = 15266.132| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.19 r_work: 0.3756 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4539 Z= 0.123 Angle : 0.478 5.017 6192 Z= 0.256 Chirality : 0.038 0.376 691 Planarity : 0.004 0.038 751 Dihedral : 5.012 59.317 602 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.52 % Allowed : 20.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.37), residues: 543 helix: 1.37 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.18 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.009 0.001 PHE A 110 TRP 0.007 0.001 TRP A 553 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4538) covalent geometry : angle 0.47794 ( 6190) SS BOND : bond 0.00239 ( 1) SS BOND : angle 0.86234 ( 2) hydrogen bonds : bond 0.04442 ( 301) hydrogen bonds : angle 4.55445 ( 861) *********************** 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 77 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.126 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: 0.8719 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 245 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7736 (t) REVERT: A 313 THR cc_start: 0.9013 (t) cc_final: 0.8606 (p) REVERT: A 352 ILE cc_start: 0.7945 (mm) cc_final: 0.7665 (mt) REVERT: A 395 ILE cc_start: 0.8341 (mt) cc_final: 0.8077 (mt) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.0918 time to fit residues: 9.2244 Evaluate side-chains 72 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.183618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157076 restraints weight = 15458.111| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.26 r_work: 0.3705 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4539 Z= 0.160 Angle : 0.509 5.189 6192 Z= 0.276 Chirality : 0.039 0.379 691 Planarity : 0.004 0.037 751 Dihedral : 5.013 54.109 602 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.37), residues: 543 helix: 1.35 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.01 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.012 0.001 PHE A 362 TRP 0.009 0.001 TRP A 80 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4538) covalent geometry : angle 0.50889 ( 6190) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.91114 ( 2) hydrogen bonds : bond 0.04784 ( 301) hydrogen bonds : angle 4.65024 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 229 ASP cc_start: 0.7627 (t0) cc_final: 0.7392 (t0) REVERT: A 245 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7628 (t) REVERT: A 352 ILE cc_start: 0.7883 (mm) cc_final: 0.7625 (mt) REVERT: A 395 ILE cc_start: 0.8366 (mt) cc_final: 0.8095 (mt) REVERT: A 518 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7807 (mtp85) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.0888 time to fit residues: 8.7042 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 : 0.127 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.182212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156566 restraints weight = 14848.709| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.14 r_work: 0.3735 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4539 Z= 0.125 Angle : 0.474 4.926 6192 Z= 0.254 Chirality : 0.039 0.377 691 Planarity : 0.004 0.039 751 Dihedral : 4.819 52.843 602 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.52 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.37), residues: 543 helix: 1.44 (0.26), residues: 395 sheet: None (None), residues: 0 loop : -0.04 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.010 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4538) covalent geometry : angle 0.47425 ( 6190) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.83648 ( 2) hydrogen bonds : bond 0.04445 ( 301) hydrogen bonds : angle 4.54432 ( 861) *********************** 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 76 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.124 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: 0.8838 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 229 ASP cc_start: 0.7744 (t70) cc_final: 0.7445 (t0) REVERT: A 245 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7730 (t) REVERT: A 313 THR cc_start: 0.9016 (t) cc_final: 0.8629 (p) REVERT: A 352 ILE cc_start: 0.7940 (mm) cc_final: 0.7697 (mt) REVERT: A 395 ILE cc_start: 0.8407 (mt) cc_final: 0.8149 (mt) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.0740 time to fit residues: 7.5057 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 : 0.119 ------------------------------------------------------------------------------- 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 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 563 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 10.9990 chunk 13 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.186236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160306 restraints weight = 15242.077| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.20 r_work: 0.3736 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4539 Z= 0.120 Angle : 0.464 4.870 6192 Z= 0.249 Chirality : 0.039 0.377 691 Planarity : 0.004 0.040 751 Dihedral : 4.680 51.988 602 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.17 % Allowed : 20.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.37), residues: 543 helix: 1.52 (0.26), residues: 397 sheet: None (None), residues: 0 loop : 0.12 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.018 0.001 PHE A 207 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4538) covalent geometry : angle 0.46433 ( 6190) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.80510 ( 2) hydrogen bonds : bond 0.04249 ( 301) hydrogen bonds : angle 4.44689 ( 861) *********************** 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 83 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.128 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: 0.8814 (OUTLIER) cc_final: 0.7111 (t80) REVERT: A 229 ASP cc_start: 0.7741 (t70) cc_final: 0.7384 (t0) REVERT: A 245 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7725 (t) REVERT: A 303 LYS cc_start: 0.7749 (mtpt) cc_final: 0.6904 (tptm) REVERT: A 313 THR cc_start: 0.8983 (t) cc_final: 0.8584 (p) REVERT: A 352 ILE cc_start: 0.7881 (mm) cc_final: 0.7662 (mt) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.0816 time to fit residues: 9.0335 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 : 0.135 ------------------------------------------------------------------------------- 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 362 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.182318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157372 restraints weight = 14973.899| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.04 r_work: 0.3743 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4539 Z= 0.125 Angle : 0.468 4.869 6192 Z= 0.251 Chirality : 0.039 0.377 691 Planarity : 0.004 0.040 751 Dihedral : 4.698 51.358 602 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.37), residues: 543 helix: 1.59 (0.27), residues: 395 sheet: None (None), residues: 0 loop : 0.12 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.010 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4538) covalent geometry : angle 0.46826 ( 6190) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.77565 ( 2) hydrogen bonds : bond 0.04280 ( 301) hydrogen bonds : angle 4.44727 ( 861) *********************** 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 79 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.143 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: 0.8818 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 229 ASP cc_start: 0.7700 (t70) cc_final: 0.7318 (t0) REVERT: A 245 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7723 (t) REVERT: A 303 LYS cc_start: 0.7751 (mtpt) cc_final: 0.6931 (tptm) REVERT: A 313 THR cc_start: 0.9002 (t) cc_final: 0.8596 (p) REVERT: A 352 ILE cc_start: 0.7908 (mm) cc_final: 0.7669 (mt) REVERT: A 534 VAL cc_start: 0.8548 (t) cc_final: 0.8342 (t) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.0822 time to fit residues: 8.5274 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 : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL 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 46 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.186364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.160157 restraints weight = 15242.320| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.25 r_work: 0.3736 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4539 Z= 0.120 Angle : 0.467 4.774 6192 Z= 0.249 Chirality : 0.039 0.378 691 Planarity : 0.004 0.040 751 Dihedral : 4.630 50.908 602 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.52 % Allowed : 21.69 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.37), residues: 543 helix: 1.63 (0.27), residues: 395 sheet: None (None), residues: 0 loop : 0.25 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.010 0.001 PHE A 207 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4538) covalent geometry : angle 0.46665 ( 6190) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.76001 ( 2) hydrogen bonds : bond 0.04216 ( 301) hydrogen bonds : angle 4.43064 ( 861) *********************** 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: 7 poor density : 68 time to evaluate : 0.247 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 229 ASP cc_start: 0.7591 (t70) cc_final: 0.7205 (t0) REVERT: A 245 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7567 (t) REVERT: A 303 LYS cc_start: 0.7716 (mtpt) cc_final: 0.6977 (tptm) REVERT: A 313 THR cc_start: 0.8925 (t) cc_final: 0.8505 (p) REVERT: A 352 ILE cc_start: 0.7833 (mm) cc_final: 0.7589 (mt) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1241 time to fit residues: 12.3599 Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 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 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7884 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.182288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157384 restraints weight = 14834.837| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.04 r_work: 0.3745 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2152 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= 0.125 Angle : 0.472 4.780 6192 Z= 0.252 Chirality : 0.039 0.379 691 Planarity : 0.004 0.040 751 Dihedral : 4.195 25.184 600 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.30 % Allowed : 21.91 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.37), residues: 543 helix: 1.61 (0.26), residues: 395 sheet: None (None), residues: 0 loop : 0.27 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.010 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4538) covalent geometry : angle 0.47185 ( 6190) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.75750 ( 2) hydrogen bonds : bond 0.04252 ( 301) hydrogen bonds : angle 4.44989 ( 861) *********************** 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: 6 poor density : 72 time to evaluate : 0.242 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 229 ASP cc_start: 0.7946 (t70) cc_final: 0.7592 (t0) REVERT: A 245 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7685 (t) REVERT: A 303 LYS cc_start: 0.7712 (mtpt) cc_final: 0.6977 (tptm) REVERT: A 313 THR cc_start: 0.9015 (t) cc_final: 0.8614 (p) REVERT: A 352 ILE cc_start: 0.7985 (mm) cc_final: 0.7741 (mt) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.1273 time to fit residues: 13.3165 Evaluate side-chains 76 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE 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 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.191751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.164281 restraints weight = 15414.828| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.35 r_work: 0.3725 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4539 Z= 0.129 Angle : 0.475 4.772 6192 Z= 0.254 Chirality : 0.039 0.380 691 Planarity : 0.004 0.040 751 Dihedral : 4.238 25.668 600 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.30 % Allowed : 21.91 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.37), residues: 543 helix: 1.61 (0.27), residues: 392 sheet: None (None), residues: 0 loop : 0.18 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 151 PHE 0.013 0.001 PHE A 207 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4538) covalent geometry : angle 0.47528 ( 6190) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.75462 ( 2) hydrogen bonds : bond 0.04306 ( 301) hydrogen bonds : angle 4.47194 ( 861) ********************** 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 81 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.217 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 229 ASP cc_start: 0.7803 (t70) cc_final: 0.7387 (t0) REVERT: A 245 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7596 (t) REVERT: A 303 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7014 (tptm) REVERT: A 313 THR cc_start: 0.8943 (t) cc_final: 0.8527 (p) REVERT: A 352 ILE cc_start: 0.7917 (mm) cc_final: 0.7673 (mt) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.1155 time to fit residues: 12.6127 Evaluate side-chains 77 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 459 PHE 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 52 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.182682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156452 restraints weight = 15384.226| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.25 r_work: 0.3695 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4539 Z= 0.167 Angle : 0.510 4.960 6192 Z= 0.276 Chirality : 0.040 0.382 691 Planarity : 0.004 0.040 751 Dihedral : 4.579 27.392 600 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.52 % Allowed : 22.34 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.37), residues: 543 helix: 1.52 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.12 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.021 0.001 TYR A 151 PHE 0.011 0.001 PHE A 362 TRP 0.010 0.001 TRP A 80 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4538) covalent geometry : angle 0.50962 ( 6190) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.74194 ( 2) hydrogen bonds : bond 0.04710 ( 301) hydrogen bonds : angle 4.61914 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.42 seconds wall clock time: 34 minutes 15.11 seconds (2055.11 seconds total)