Starting phenix.real_space_refine on Tue Feb 11 01:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc3_40336/02_2025/8sc3_40336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc3_40336/02_2025/8sc3_40336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc3_40336/02_2025/8sc3_40336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc3_40336/02_2025/8sc3_40336.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc3_40336/02_2025/8sc3_40336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc3_40336/02_2025/8sc3_40336.cif" } resolution = 3.24 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2284 2.51 5 N 559 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3463 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3441 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'ZVJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.73, per 1000 atoms: 0.79 Number of scatterers: 3463 At special positions: 0 Unit cell: (89.64, 83, 63.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 590 8.00 N 559 7.00 C 2284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " 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: 0.98 Conformation dependent library (CDL) restraints added in 387.7 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 82.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 145 through 173 removed outlier: 4.053A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.600A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 4.241A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 271 - end of helix removed outlier: 3.560A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.579A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 4.101A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.862A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 4.116A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 487 removed outlier: 4.432A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.652A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 256 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1063 1.35 - 1.47: 914 1.47 - 1.59: 1531 1.59 - 1.71: 1 1.71 - 1.83: 45 Bond restraints: 3554 Sorted by residual: bond pdb=" C08 ZVJ A 601 " pdb=" O09 ZVJ A 601 " ideal model delta sigma weight residual 1.348 1.451 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C15 ZVJ A 601 " pdb=" C16 ZVJ A 601 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C11 ZVJ A 601 " pdb=" O12 ZVJ A 601 " ideal model delta sigma weight residual 1.349 1.438 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C19 ZVJ A 601 " pdb=" O22 ZVJ A 601 " ideal model delta sigma weight residual 1.350 1.428 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C04 ZVJ A 601 " pdb=" C05 ZVJ A 601 " ideal model delta sigma weight residual 1.540 1.482 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 3549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4718 1.69 - 3.37: 109 3.37 - 5.06: 11 5.06 - 6.75: 4 6.75 - 8.43: 1 Bond angle restraints: 4843 Sorted by residual: angle pdb=" C05 ZVJ A 601 " pdb=" C04 ZVJ A 601 " pdb=" N03 ZVJ A 601 " ideal model delta sigma weight residual 109.71 118.14 -8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" CA VAL A 37 " pdb=" CB VAL A 37 " pdb=" CG1 VAL A 37 " ideal model delta sigma weight residual 110.40 115.00 -4.60 1.70e+00 3.46e-01 7.34e+00 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" CB VAL A 37 " ideal model delta sigma weight residual 112.26 109.10 3.16 1.29e+00 6.01e-01 6.00e+00 angle pdb=" CA CYS A 102 " pdb=" CB CYS A 102 " pdb=" SG CYS A 102 " ideal model delta sigma weight residual 114.40 119.97 -5.57 2.30e+00 1.89e-01 5.87e+00 angle pdb=" N ARG A 462 " pdb=" CA ARG A 462 " pdb=" C ARG A 462 " ideal model delta sigma weight residual 111.37 115.02 -3.65 1.65e+00 3.67e-01 4.90e+00 ... (remaining 4838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 1942 16.82 - 33.63: 90 33.63 - 50.44: 29 50.44 - 67.26: 4 67.26 - 84.07: 2 Dihedral angle restraints: 2067 sinusoidal: 794 harmonic: 1273 Sorted by residual: dihedral pdb=" CA ASN A 374 " pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " pdb=" CD GLU A 515 " pdb=" OE1 GLU A 515 " ideal model delta sinusoidal sigma weight residual 0.00 -84.07 84.07 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU A 489 " pdb=" CG GLU A 489 " pdb=" CD GLU A 489 " pdb=" OE1 GLU A 489 " ideal model delta sinusoidal sigma weight residual 0.00 81.08 -81.08 1 3.00e+01 1.11e-03 9.01e+00 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 474 0.052 - 0.104: 76 0.104 - 0.156: 11 0.156 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 562 Sorted by residual: chirality pdb=" C02 ZVJ A 601 " pdb=" C01 ZVJ A 601 " pdb=" C15 ZVJ A 601 " pdb=" N03 ZVJ A 601 " both_signs ideal model delta sigma weight residual False -2.45 -2.71 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 559 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 406 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C MET A 406 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 406 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 407 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 28 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LEU A 28 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 28 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 29 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 239 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C MET A 239 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 239 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 240 " 0.013 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 294 2.74 - 3.28: 3746 3.28 - 3.82: 5805 3.82 - 4.36: 6758 4.36 - 4.90: 11725 Nonbonded interactions: 28328 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.206 3.040 nonbonded pdb=" NH1 ARG A 90 " pdb=" OD2 ASP A 123 " model vdw 2.407 3.120 nonbonded pdb=" O ALA A 194 " pdb=" NH1 ARG A 262 " model vdw 2.409 3.120 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.469 3.040 nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 216 " model vdw 2.488 3.040 ... (remaining 28323 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: 1.110 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.060 Find NCS groups from input model: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.005 0.103 3554 Z= 0.289 Angle : 0.644 8.433 4843 Z= 0.372 Chirality : 0.039 0.259 562 Planarity : 0.006 0.037 597 Dihedral : 11.841 84.073 1244 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.38), residues: 441 helix: -0.50 (0.26), residues: 317 sheet: None (None), residues: 0 loop : 0.60 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 261 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.002 PHE A 151 TYR 0.021 0.002 TYR A 72 ARG 0.008 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8137 (m-30) cc_final: 0.7845 (m-30) REVERT: A 116 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (mp) REVERT: A 150 LEU cc_start: 0.8883 (tp) cc_final: 0.8647 (tt) REVERT: A 154 CYS cc_start: 0.8293 (m) cc_final: 0.8035 (m) REVERT: A 392 ILE cc_start: 0.8580 (mt) cc_final: 0.8255 (mt) REVERT: A 460 PHE cc_start: 0.4975 (t80) cc_final: 0.4646 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1442 time to fit residues: 23.9211 Evaluate side-chains 106 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.202209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162660 restraints weight = 4619.504| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.18 r_work: 0.3646 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3554 Z= 0.204 Angle : 0.598 5.493 4843 Z= 0.313 Chirality : 0.039 0.138 562 Planarity : 0.004 0.047 597 Dihedral : 7.258 61.432 492 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.52 % Allowed : 8.13 % Favored : 88.35 % 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: 2.21 (0.41), residues: 441 helix: 1.58 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 1.48 (0.67), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.019 0.002 PHE A 227 TYR 0.019 0.002 TYR A 240 ARG 0.005 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8562 (m-30) cc_final: 0.8228 (m-30) REVERT: A 116 LEU cc_start: 0.8549 (mt) cc_final: 0.8200 (mp) REVERT: A 200 MET cc_start: 0.7633 (mmt) cc_final: 0.7427 (mmt) REVERT: A 239 MET cc_start: 0.7230 (tpt) cc_final: 0.6625 (tpt) REVERT: A 348 PHE cc_start: 0.8067 (m-10) cc_final: 0.7814 (m-10) REVERT: A 392 ILE cc_start: 0.8670 (mt) cc_final: 0.8443 (mt) REVERT: A 410 ASN cc_start: 0.8226 (m-40) cc_final: 0.7933 (m110) REVERT: A 429 TRP cc_start: 0.7222 (p-90) cc_final: 0.6996 (p90) REVERT: A 460 PHE cc_start: 0.5759 (t80) cc_final: 0.4941 (t80) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.1332 time to fit residues: 20.9732 Evaluate side-chains 103 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.202088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161505 restraints weight = 4636.819| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.02 r_work: 0.3636 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3554 Z= 0.208 Angle : 0.602 10.264 4843 Z= 0.308 Chirality : 0.040 0.222 562 Planarity : 0.004 0.049 597 Dihedral : 7.763 91.264 492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.79 % Allowed : 10.30 % Favored : 85.91 % 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: 2.61 (0.42), residues: 441 helix: 1.83 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 1.77 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 151 TYR 0.018 0.002 TYR A 361 ARG 0.006 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8360 (m-80) cc_final: 0.8138 (m-10) REVERT: A 200 MET cc_start: 0.7584 (mmt) cc_final: 0.7381 (mmt) REVERT: A 242 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7248 (ppp) REVERT: A 348 PHE cc_start: 0.8087 (m-10) cc_final: 0.7750 (m-10) REVERT: A 351 MET cc_start: 0.7724 (mtt) cc_final: 0.6859 (tmm) REVERT: A 408 MET cc_start: 0.8535 (mtp) cc_final: 0.8317 (mtt) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.1237 time to fit residues: 17.3520 Evaluate side-chains 107 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.0020 chunk 10 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163176 restraints weight = 4652.612| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.16 r_work: 0.3647 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3554 Z= 0.193 Angle : 0.567 5.696 4843 Z= 0.298 Chirality : 0.040 0.221 562 Planarity : 0.004 0.048 597 Dihedral : 7.407 83.874 492 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.79 % Allowed : 13.01 % Favored : 83.20 % 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: 2.74 (0.42), residues: 441 helix: 1.94 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 1.76 (0.70), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.001 PHE A 391 TYR 0.017 0.002 TYR A 361 ARG 0.008 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7168 (tpt) cc_final: 0.6967 (tpt) REVERT: A 334 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: A 348 PHE cc_start: 0.8085 (m-10) cc_final: 0.7711 (m-10) REVERT: A 351 MET cc_start: 0.7670 (mtt) cc_final: 0.6817 (tmm) REVERT: A 352 TYR cc_start: 0.8095 (t80) cc_final: 0.7861 (t80) REVERT: A 408 MET cc_start: 0.8497 (mtp) cc_final: 0.8279 (mtt) REVERT: A 498 LEU cc_start: 0.8250 (mm) cc_final: 0.7930 (mm) REVERT: A 511 LEU cc_start: 0.8234 (mt) cc_final: 0.8034 (mm) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 0.1157 time to fit residues: 15.7660 Evaluate side-chains 102 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.203263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162955 restraints weight = 4713.014| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.15 r_work: 0.3644 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3554 Z= 0.194 Angle : 0.549 5.563 4843 Z= 0.291 Chirality : 0.040 0.215 562 Planarity : 0.004 0.047 597 Dihedral : 7.225 72.899 492 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.34 % Allowed : 14.63 % Favored : 81.03 % 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: 2.73 (0.42), residues: 441 helix: 1.96 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 1.69 (0.70), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 22 TYR 0.018 0.001 TYR A 361 ARG 0.009 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7595 (mmt) cc_final: 0.7383 (mmt) REVERT: A 239 MET cc_start: 0.7141 (tpt) cc_final: 0.6821 (tpt) REVERT: A 334 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: A 348 PHE cc_start: 0.8080 (m-10) cc_final: 0.7692 (m-10) REVERT: A 351 MET cc_start: 0.7693 (mtt) cc_final: 0.6821 (tmm) REVERT: A 352 TYR cc_start: 0.8110 (t80) cc_final: 0.7876 (t80) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.1103 time to fit residues: 14.1412 Evaluate side-chains 103 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.201028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161292 restraints weight = 4802.039| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.00 r_work: 0.3634 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3554 Z= 0.224 Angle : 0.581 6.008 4843 Z= 0.304 Chirality : 0.041 0.210 562 Planarity : 0.005 0.046 597 Dihedral : 7.176 72.406 492 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.34 % Allowed : 15.45 % Favored : 80.22 % 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: 2.66 (0.42), residues: 441 helix: 1.86 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 1.80 (0.71), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.019 0.001 PHE A 391 TYR 0.019 0.002 TYR A 361 ARG 0.011 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7156 (tpt) cc_final: 0.6776 (tpt) REVERT: A 334 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: A 348 PHE cc_start: 0.8052 (m-10) cc_final: 0.7699 (m-10) REVERT: A 351 MET cc_start: 0.7713 (mtt) cc_final: 0.7275 (ttt) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.1221 time to fit residues: 15.8879 Evaluate side-chains 97 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.202482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162732 restraints weight = 4736.044| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.16 r_work: 0.3648 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3554 Z= 0.207 Angle : 0.579 8.826 4843 Z= 0.300 Chirality : 0.040 0.209 562 Planarity : 0.005 0.048 597 Dihedral : 7.133 70.549 492 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.34 % Allowed : 17.62 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.42), residues: 441 helix: 1.93 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 1.77 (0.71), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 460 TYR 0.018 0.002 TYR A 361 ARG 0.011 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6538 (m100) cc_final: 0.6167 (m100) REVERT: A 239 MET cc_start: 0.7081 (tpt) cc_final: 0.6772 (tpt) REVERT: A 334 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: A 348 PHE cc_start: 0.8046 (m-10) cc_final: 0.7667 (m-10) REVERT: A 351 MET cc_start: 0.7703 (mtt) cc_final: 0.7244 (ttt) outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 0.1205 time to fit residues: 15.0561 Evaluate side-chains 98 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.203761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164255 restraints weight = 4754.021| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.16 r_work: 0.3667 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3554 Z= 0.187 Angle : 0.588 8.338 4843 Z= 0.299 Chirality : 0.040 0.206 562 Planarity : 0.005 0.048 597 Dihedral : 6.983 71.660 492 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.52 % Allowed : 18.70 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.42), residues: 441 helix: 1.96 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 1.81 (0.71), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.022 0.001 PHE A 391 TYR 0.020 0.001 TYR A 361 ARG 0.012 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7082 (tpt) cc_final: 0.6739 (tpt) REVERT: A 334 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: A 348 PHE cc_start: 0.8034 (m-10) cc_final: 0.7648 (m-10) REVERT: A 351 MET cc_start: 0.7716 (mtt) cc_final: 0.7238 (ttt) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1248 time to fit residues: 14.9476 Evaluate side-chains 96 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.0030 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.204644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.165182 restraints weight = 4620.150| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.19 r_work: 0.3670 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3554 Z= 0.182 Angle : 0.582 8.083 4843 Z= 0.298 Chirality : 0.040 0.198 562 Planarity : 0.005 0.048 597 Dihedral : 6.882 71.370 492 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.25 % Allowed : 19.51 % Favored : 77.24 % 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: 2.67 (0.42), residues: 441 helix: 1.82 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 1.96 (0.74), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.016 0.001 PHE A 460 TYR 0.018 0.001 TYR A 361 ARG 0.013 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8674 (mt) cc_final: 0.8282 (mp) REVERT: A 239 MET cc_start: 0.7014 (tpt) cc_final: 0.6747 (tpt) REVERT: A 334 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 348 PHE cc_start: 0.8039 (m-10) cc_final: 0.7655 (m-10) REVERT: A 351 MET cc_start: 0.7690 (mtt) cc_final: 0.7223 (ttt) outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.1143 time to fit residues: 13.6164 Evaluate side-chains 95 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.205197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165667 restraints weight = 4695.890| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.24 r_work: 0.3677 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3554 Z= 0.180 Angle : 0.592 7.496 4843 Z= 0.301 Chirality : 0.041 0.196 562 Planarity : 0.005 0.047 597 Dihedral : 6.913 71.885 492 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.71 % Allowed : 20.87 % Favored : 76.42 % 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: 2.61 (0.42), residues: 441 helix: 1.79 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 1.90 (0.73), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 354 HIS 0.002 0.001 HIS A 49 PHE 0.026 0.001 PHE A 391 TYR 0.019 0.001 TYR A 361 ARG 0.012 0.001 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8679 (mt) cc_final: 0.8288 (mp) REVERT: A 123 ASP cc_start: 0.8288 (t0) cc_final: 0.7981 (t0) REVERT: A 233 ARG cc_start: 0.7654 (ptp-170) cc_final: 0.7402 (ptp-170) REVERT: A 239 MET cc_start: 0.7007 (tpt) cc_final: 0.6709 (tpt) REVERT: A 334 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 348 PHE cc_start: 0.8042 (m-10) cc_final: 0.7651 (m-10) REVERT: A 351 MET cc_start: 0.7680 (mtt) cc_final: 0.7199 (ttt) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 0.1262 time to fit residues: 15.7024 Evaluate side-chains 98 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.4980 chunk 2 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.204445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164980 restraints weight = 4693.277| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.22 r_work: 0.3667 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3554 Z= 0.190 Angle : 0.593 8.277 4843 Z= 0.307 Chirality : 0.042 0.189 562 Planarity : 0.005 0.050 597 Dihedral : 6.859 68.652 492 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.44 % Allowed : 21.95 % Favored : 75.61 % 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: 2.63 (0.42), residues: 441 helix: 1.81 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 1.88 (0.73), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.016 0.001 PHE A 460 TYR 0.020 0.002 TYR A 361 ARG 0.014 0.001 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.02 seconds wall clock time: 38 minutes 31.38 seconds (2311.38 seconds total)