Starting phenix.real_space_refine on Fri Dec 27 07:58:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc3_40336/12_2024/8sc3_40336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc3_40336/12_2024/8sc3_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_40336/12_2024/8sc3_40336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc3_40336/12_2024/8sc3_40336.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc3_40336/12_2024/8sc3_40336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc3_40336/12_2024/8sc3_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-5532/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: 2.94, per 1000 atoms: 0.85 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: 1.23 Conformation dependent library (CDL) restraints added in 637.5 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: 0.34 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: 1.30 Time building geometry restraints manager: 1.05 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: 0.710 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- 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 : 0.376 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: 0.1547 time to fit residues: 25.7482 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 : 0.329 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8070 (m-30) cc_final: 0.7730 (m-30) REVERT: A 116 LEU cc_start: 0.8560 (mt) cc_final: 0.8221 (mp) REVERT: A 239 MET cc_start: 0.7245 (tpt) cc_final: 0.6712 (tpt) REVERT: A 410 ASN cc_start: 0.8250 (m-40) cc_final: 0.7991 (m110) REVERT: A 460 PHE cc_start: 0.5177 (t80) cc_final: 0.4287 (t80) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.1431 time to fit residues: 22.6673 Evaluate side-chains 102 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3554 Z= 0.178 Angle : 0.588 9.984 4843 Z= 0.302 Chirality : 0.039 0.216 562 Planarity : 0.004 0.050 597 Dihedral : 7.737 91.841 492 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.52 % Allowed : 10.57 % 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: 2.73 (0.42), residues: 441 helix: 1.94 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 1.75 (0.67), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 348 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 116 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8097 (m-30) cc_final: 0.7791 (m-30) REVERT: A 242 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7021 (ppp) REVERT: A 351 MET cc_start: 0.6930 (mtt) cc_final: 0.6585 (tmm) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.1217 time to fit residues: 16.9584 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 : 0.456 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.0050 chunk 30 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3836 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= 0.178 Angle : 0.555 5.635 4843 Z= 0.291 Chirality : 0.039 0.218 562 Planarity : 0.004 0.048 597 Dihedral : 7.408 86.055 492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.52 % Allowed : 13.55 % Favored : 82.93 % 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: 2.80 (0.42), residues: 441 helix: 2.00 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 1.74 (0.69), residues: 122 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 0.014 0.002 PHE A 348 TYR 0.016 0.001 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 113 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8085 (m-30) cc_final: 0.7811 (m-30) REVERT: A 334 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: A 351 MET cc_start: 0.6931 (mtt) cc_final: 0.6597 (tmm) REVERT: A 498 LEU cc_start: 0.8096 (mm) cc_final: 0.7818 (mm) outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 0.1224 time to fit residues: 16.6157 Evaluate side-chains 101 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 472 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4107 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= 0.201 Angle : 0.580 5.301 4843 Z= 0.303 Chirality : 0.040 0.209 562 Planarity : 0.005 0.047 597 Dihedral : 7.265 74.931 492 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.79 % Allowed : 13.28 % Favored : 82.93 % 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: 2.68 (0.42), residues: 441 helix: 1.89 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.74 (0.69), residues: 120 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 0.017 0.001 PHE A 348 TYR 0.018 0.002 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 107 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8099 (m-30) cc_final: 0.7855 (m-30) REVERT: A 242 MET cc_start: 0.7356 (ptt) cc_final: 0.6967 (ppp) REVERT: A 334 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: A 351 MET cc_start: 0.6974 (mtt) cc_final: 0.6620 (tmm) REVERT: A 352 TYR cc_start: 0.8122 (t80) cc_final: 0.7902 (t80) REVERT: A 498 LEU cc_start: 0.8089 (mm) cc_final: 0.7788 (mm) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.1103 time to fit residues: 14.2900 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 : 0.335 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4273 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= 0.195 Angle : 0.567 6.003 4843 Z= 0.302 Chirality : 0.041 0.210 562 Planarity : 0.005 0.048 597 Dihedral : 7.172 75.797 492 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.34 % Allowed : 14.09 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.42), residues: 441 helix: 1.96 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.71 (0.69), residues: 120 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 0.019 0.001 PHE A 391 TYR 0.017 0.001 TYR A 361 ARG 0.009 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 109 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8102 (m-30) cc_final: 0.7834 (m-30) REVERT: A 239 MET cc_start: 0.7167 (tpt) cc_final: 0.6631 (tpt) REVERT: A 242 MET cc_start: 0.7233 (ptt) cc_final: 0.6875 (ppp) REVERT: A 334 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: A 351 MET cc_start: 0.6920 (mtt) cc_final: 0.6570 (tmm) REVERT: A 352 TYR cc_start: 0.8069 (t80) cc_final: 0.7846 (t80) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 0.1052 time to fit residues: 13.9175 Evaluate side-chains 95 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4583 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= 0.193 Angle : 0.584 7.541 4843 Z= 0.304 Chirality : 0.041 0.208 562 Planarity : 0.005 0.047 597 Dihedral : 7.141 75.156 492 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.25 % Allowed : 17.07 % Favored : 79.67 % 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: 1.97 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 1.65 (0.68), 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 0.020 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 101 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.380 Fit side-chains REVERT: A 47 ASP cc_start: 0.8040 (m-30) cc_final: 0.7775 (m-30) REVERT: A 334 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: A 457 TYR cc_start: 0.6599 (m-80) cc_final: 0.6314 (m-80) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.1177 time to fit residues: 14.7775 Evaluate side-chains 95 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 20 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4708 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= 0.224 Angle : 0.600 6.519 4843 Z= 0.314 Chirality : 0.042 0.238 562 Planarity : 0.005 0.046 597 Dihedral : 7.157 74.112 492 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.34 % Allowed : 17.34 % Favored : 78.32 % 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: 2.68 (0.42), residues: 441 helix: 1.90 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 1.72 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.023 0.001 PHE A 391 TYR 0.020 0.002 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 102 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8088 (m-30) cc_final: 0.7817 (m-30) REVERT: A 334 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: A 457 TYR cc_start: 0.6549 (m-80) cc_final: 0.6276 (m-80) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1154 time to fit residues: 14.5349 Evaluate side-chains 97 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 102 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4759 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= 0.225 Angle : 0.613 6.210 4843 Z= 0.318 Chirality : 0.043 0.254 562 Planarity : 0.005 0.047 597 Dihedral : 7.142 71.653 492 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.79 % Allowed : 18.70 % Favored : 77.51 % 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: 2.69 (0.42), residues: 441 helix: 1.86 (0.28), residues: 323 sheet: None (None), residues: 0 loop : 1.90 (0.70), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 460 TYR 0.019 0.002 TYR A 361 ARG 0.010 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 100 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.363 Fit side-chains REVERT: A 47 ASP cc_start: 0.8050 (m-30) cc_final: 0.7757 (m-30) REVERT: A 123 ASP cc_start: 0.7844 (t0) cc_final: 0.7542 (t0) REVERT: A 334 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: A 447 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7594 (tp40) REVERT: A 457 TYR cc_start: 0.6557 (m-80) cc_final: 0.6308 (m-80) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.1021 time to fit residues: 12.8675 Evaluate side-chains 98 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 102 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4877 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= 0.216 Angle : 0.601 6.541 4843 Z= 0.314 Chirality : 0.043 0.255 562 Planarity : 0.005 0.047 597 Dihedral : 7.064 68.151 492 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.98 % Allowed : 20.05 % Favored : 76.96 % 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: 2.68 (0.42), residues: 441 helix: 1.83 (0.28), residues: 323 sheet: None (None), residues: 0 loop : 1.95 (0.71), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.026 0.001 PHE A 391 TYR 0.019 0.002 TYR A 361 ARG 0.010 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 97 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.380 Fit side-chains REVERT: A 47 ASP cc_start: 0.8061 (m-30) cc_final: 0.7779 (m-30) REVERT: A 123 ASP cc_start: 0.7836 (t0) cc_final: 0.7533 (t0) REVERT: A 447 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7548 (tp40) REVERT: A 457 TYR cc_start: 0.6527 (m-80) cc_final: 0.6280 (m-80) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.1044 time to fit residues: 12.6920 Evaluate side-chains 94 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 204 LEU 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 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 4 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.202601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163282 restraints weight = 4722.171| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.02 r_work: 0.3673 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3554 Z= 0.222 Angle : 0.619 7.524 4843 Z= 0.321 Chirality : 0.043 0.249 562 Planarity : 0.005 0.047 597 Dihedral : 7.003 65.343 492 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.98 % Allowed : 20.05 % Favored : 76.96 % 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: 2.60 (0.42), residues: 441 helix: 1.75 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 2.01 (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 260 PHE 0.016 0.001 PHE A 460 TYR 0.019 0.002 TYR A 361 ARG 0.009 0.001 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1186.69 seconds wall clock time: 22 minutes 26.31 seconds (1346.31 seconds total)