Starting phenix.real_space_refine on Tue Feb 13 21:21:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/02_2024/8b0p_15791_updated.pdb" } resolution = 2.86 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= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3779 atoms to isotropic. 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 14 5.16 5 C 2652 2.51 5 N 655 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4016 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3911 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 36, 'TRANS': 468} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Unusual residues: {'IG7': 1} Inner-chain residues flagged as termini: ['pdbres="LYS B 6 "'] Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="LYS B 6 " pdbres="IG7 B 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'IG7:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.88, per 1000 atoms: 0.72 Number of scatterers: 4016 At special positions: 0 Unit cell: (57.82, 83.426, 85.904, 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 14 16.00 O 695 8.00 N 655 7.00 C 2652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 851.3 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SER B 2 " pdb=" CB LYS B 3 " Number of C-beta restraints generated: 936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 2 sheets defined 48.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.737A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.682A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.573A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.574A pdb=" N ALA A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 removed outlier: 4.179A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 161 through 167 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 169 through 189 removed outlier: 3.553A pdb=" N PHE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 210 Proline residue: A 205 - end of helix removed outlier: 4.717A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 241 through 256 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 421 through 436 removed outlier: 3.661A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 489 through 506 Processing sheet with id= A, first strand: chain 'A' and resid 468 through 474 removed outlier: 6.441A pdb=" N LEU A 262 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL A 227 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 264 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER A 294 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N TRP A 265 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 296 " --> pdb=" O TRP A 265 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 382 through 386 removed outlier: 7.370A pdb=" N TYR A 406 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 385 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 408 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR A 409 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 441 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER A 411 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 443 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 460 " --> pdb=" O VAL A 451 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 471 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: 1.10 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 649 1.32 - 1.45: 1103 1.45 - 1.57: 2348 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4126 Sorted by residual: bond pdb=" C02 IG7 B 1 " pdb=" N01 IG7 B 1 " ideal model delta sigma weight residual 1.460 1.334 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C21 IG7 B 1 " pdb=" O20 IG7 B 1 " ideal model delta sigma weight residual 1.415 1.327 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C42 IG7 B 1 " pdb=" O43 IG7 B 1 " ideal model delta sigma weight residual 1.402 1.458 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C44 IG7 B 1 " pdb=" O43 IG7 B 1 " ideal model delta sigma weight residual 1.402 1.346 0.056 2.00e-02 2.50e+03 7.78e+00 bond pdb=" C22 IG7 B 1 " pdb=" C23 IG7 B 1 " ideal model delta sigma weight residual 1.549 1.494 0.055 2.00e-02 2.50e+03 7.44e+00 ... (remaining 4121 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 181 107.04 - 113.78: 2270 113.78 - 120.52: 1588 120.52 - 127.26: 1515 127.26 - 134.00: 69 Bond angle restraints: 5623 Sorted by residual: angle pdb=" C22 IG7 B 1 " pdb=" C21 IG7 B 1 " pdb=" O20 IG7 B 1 " ideal model delta sigma weight residual 119.92 111.28 8.64 3.00e+00 1.11e-01 8.30e+00 angle pdb=" C45 IG7 B 1 " pdb=" C44 IG7 B 1 " pdb=" O43 IG7 B 1 " ideal model delta sigma weight residual 119.98 111.67 8.31 3.00e+00 1.11e-01 7.67e+00 angle pdb=" C39 IG7 B 1 " pdb=" S40 IG7 B 1 " pdb=" C41 IG7 B 1 " ideal model delta sigma weight residual 109.52 101.24 8.28 3.00e+00 1.11e-01 7.62e+00 angle pdb=" O LYS B 6 " pdb=" C LYS B 6 " pdb=" OXT LYS B 6 " ideal model delta sigma weight residual 118.00 125.52 -7.52 3.00e+00 1.11e-01 6.28e+00 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 113.07 109.73 3.34 1.36e+00 5.41e-01 6.02e+00 ... (remaining 5618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 2319 17.79 - 35.59: 78 35.59 - 53.38: 20 53.38 - 71.17: 8 71.17 - 88.96: 2 Dihedral angle restraints: 2427 sinusoidal: 966 harmonic: 1461 Sorted by residual: dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS B 5 " pdb=" C LYS B 5 " pdb=" N LYS B 6 " pdb=" CA LYS B 6 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" N PHE A 82 " pdb=" CA PHE A 82 " pdb=" CB PHE A 82 " pdb=" CG PHE A 82 " ideal model delta sinusoidal sigma weight residual 60.00 1.55 58.45 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 632 1.003 - 2.006: 0 2.006 - 3.009: 0 3.009 - 4.012: 0 4.012 - 5.015: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA SER B 2 " pdb=" N SER B 2 " pdb=" C SER B 2 " pdb=" CB SER B 2 " both_signs ideal model delta sigma weight residual False 2.51 -2.50 5.01 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C42 IG7 B 1 " pdb=" C19 IG7 B 1 " pdb=" C41 IG7 B 1 " pdb=" O43 IG7 B 1 " both_signs ideal model delta sigma weight residual False -2.53 2.31 -4.84 2.00e-01 2.50e+01 5.86e+02 chirality pdb=" CA LYS B 3 " pdb=" N LYS B 3 " pdb=" C LYS B 3 " pdb=" CB LYS B 3 " both_signs ideal model delta sigma weight residual False 2.51 -2.31 4.82 2.00e-01 2.50e+01 5.82e+02 ... (remaining 632 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 IG7 B 1 " -0.041 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C03 IG7 B 1 " 0.103 2.00e-02 2.50e+03 pdb=" C38 IG7 B 1 " 0.137 2.00e-02 2.50e+03 pdb=" N01 IG7 B 1 " -0.183 2.00e-02 2.50e+03 pdb=" O18 IG7 B 1 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 88 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 422 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.020 5.00e-02 4.00e+02 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 713 2.77 - 3.30: 3942 3.30 - 3.83: 6872 3.83 - 4.37: 8679 4.37 - 4.90: 14618 Nonbonded interactions: 34824 Sorted by model distance: nonbonded pdb=" OE1 GLN A 133 " pdb=" OG1 THR A 495 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.277 2.440 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 143 " pdb=" OG1 THR A 144 " model vdw 2.330 2.440 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.393 2.520 ... (remaining 34819 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 3.030 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.100 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 0.126 4126 Z= 0.293 Angle : 0.712 8.642 5623 Z= 0.306 Chirality : 0.339 5.015 635 Planarity : 0.006 0.114 703 Dihedral : 10.465 88.965 1491 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.16 % Favored : 96.64 % Rotamer: Outliers : 0.97 % Allowed : 2.68 % Favored : 96.35 % Cbeta Deviations : 0.43 % 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: -0.43 (0.36), residues: 506 helix: 0.31 (0.32), residues: 251 sheet: -0.62 (0.65), residues: 62 loop : -0.80 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.007 0.001 PHE A 28 TYR 0.007 0.001 TYR A 313 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.470 Fit side-chains REVERT: A 82 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5760 (p90) REVERT: A 170 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6921 (mp0) REVERT: A 331 ASP cc_start: 0.7012 (m-30) cc_final: 0.6800 (m-30) outliers start: 4 outliers final: 0 residues processed: 50 average time/residue: 0.6981 time to fit residues: 37.2337 Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4126 Z= 0.224 Angle : 0.595 10.504 5623 Z= 0.293 Chirality : 0.066 1.243 635 Planarity : 0.005 0.036 703 Dihedral : 9.392 80.438 600 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.16 % Favored : 96.44 % Rotamer: Outliers : 2.19 % Allowed : 5.11 % Favored : 92.70 % Cbeta Deviations : 0.21 % 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: 0.04 (0.37), residues: 506 helix: 0.85 (0.33), residues: 257 sheet: -0.30 (0.64), residues: 56 loop : -0.92 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 492 HIS 0.001 0.000 HIS A 425 PHE 0.012 0.001 PHE A 426 TYR 0.006 0.001 TYR A 313 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.487 Fit side-chains REVERT: A 82 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.5631 (p90) REVERT: A 121 TRP cc_start: 0.7986 (p-90) cc_final: 0.7718 (p-90) outliers start: 9 outliers final: 2 residues processed: 50 average time/residue: 0.6961 time to fit residues: 37.2168 Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0070 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4126 Z= 0.171 Angle : 0.538 6.393 5623 Z= 0.261 Chirality : 0.051 0.717 635 Planarity : 0.004 0.035 703 Dihedral : 8.596 77.952 600 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.16 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 7.79 % Favored : 90.27 % Cbeta Deviations : 0.21 % 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: 0.25 (0.38), residues: 506 helix: 1.08 (0.34), residues: 258 sheet: -0.13 (0.64), residues: 56 loop : -0.94 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.006 0.001 TYR A 313 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.419 Fit side-chains REVERT: A 82 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5834 (p90) outliers start: 8 outliers final: 3 residues processed: 42 average time/residue: 0.6906 time to fit residues: 31.0046 Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4126 Z= 0.192 Angle : 0.535 6.085 5623 Z= 0.260 Chirality : 0.048 0.531 635 Planarity : 0.004 0.036 703 Dihedral : 8.260 76.767 600 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.95 % Allowed : 9.00 % Favored : 89.05 % Cbeta Deviations : 0.21 % 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: 0.35 (0.38), residues: 506 helix: 1.14 (0.34), residues: 257 sheet: -0.15 (0.63), residues: 56 loop : -0.82 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 426 TYR 0.007 0.001 TYR A 313 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 1.230 Fit side-chains REVERT: A 82 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5853 (p90) outliers start: 8 outliers final: 1 residues processed: 42 average time/residue: 0.7704 time to fit residues: 35.0591 Evaluate side-chains 37 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4126 Z= 0.149 Angle : 0.510 6.055 5623 Z= 0.246 Chirality : 0.045 0.414 635 Planarity : 0.004 0.037 703 Dihedral : 7.993 75.787 600 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.22 % Allowed : 10.22 % Favored : 88.56 % Cbeta Deviations : 0.21 % 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: 0.51 (0.38), residues: 506 helix: 1.27 (0.34), residues: 258 sheet: 0.20 (0.64), residues: 54 loop : -0.85 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.009 0.001 PHE A 174 TYR 0.006 0.001 TYR A 313 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.461 Fit side-chains REVERT: A 82 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6000 (p90) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.8744 time to fit residues: 38.1058 Evaluate side-chains 38 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4126 Z= 0.347 Angle : 0.594 6.160 5623 Z= 0.291 Chirality : 0.049 0.407 635 Planarity : 0.005 0.034 703 Dihedral : 8.407 73.414 600 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.73 % Allowed : 12.17 % Favored : 87.10 % Cbeta Deviations : 0.21 % 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: 0.10 (0.37), residues: 506 helix: 0.89 (0.33), residues: 254 sheet: -0.25 (0.63), residues: 56 loop : -0.86 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.002 0.001 HIS A 425 PHE 0.013 0.002 PHE A 426 TYR 0.008 0.001 TYR A 104 ARG 0.003 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.464 Fit side-chains REVERT: A 82 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5897 (p90) REVERT: A 121 TRP cc_start: 0.8038 (p-90) cc_final: 0.7775 (p-90) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.6212 time to fit residues: 24.9239 Evaluate side-chains 36 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7975 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4126 Z= 0.197 Angle : 0.535 6.098 5623 Z= 0.262 Chirality : 0.045 0.379 635 Planarity : 0.004 0.038 703 Dihedral : 8.126 69.733 600 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.97 % Allowed : 12.17 % Favored : 86.86 % 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: 0.29 (0.38), residues: 506 helix: 1.05 (0.34), residues: 257 sheet: -0.23 (0.64), residues: 56 loop : -0.77 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.010 0.001 PHE A 174 TYR 0.007 0.001 TYR A 313 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.485 Fit side-chains REVERT: A 82 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5891 (p90) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.7291 time to fit residues: 28.2687 Evaluate side-chains 36 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4126 Z= 0.212 Angle : 0.540 6.187 5623 Z= 0.264 Chirality : 0.045 0.347 635 Planarity : 0.004 0.037 703 Dihedral : 8.119 68.080 600 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.22 % Allowed : 11.68 % Favored : 87.10 % 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: 0.33 (0.37), residues: 506 helix: 1.13 (0.34), residues: 254 sheet: -0.26 (0.64), residues: 56 loop : -0.77 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.425 Fit side-chains REVERT: A 50 ASN cc_start: 0.7446 (m110) cc_final: 0.6769 (t0) REVERT: A 82 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5927 (p90) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.7252 time to fit residues: 30.2769 Evaluate side-chains 37 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4126 Z= 0.213 Angle : 0.539 6.331 5623 Z= 0.264 Chirality : 0.045 0.334 635 Planarity : 0.004 0.037 703 Dihedral : 8.086 64.587 600 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.22 % Allowed : 11.92 % Favored : 86.86 % 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: 0.29 (0.38), residues: 506 helix: 1.05 (0.33), residues: 257 sheet: -0.24 (0.64), residues: 56 loop : -0.77 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.462 Fit side-chains REVERT: A 50 ASN cc_start: 0.7447 (m110) cc_final: 0.6765 (t0) REVERT: A 82 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5916 (p90) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.6871 time to fit residues: 28.1215 Evaluate side-chains 37 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 overall best weight: 0.3466 ------------------------------------------------------------------------------- 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: 0.7922 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4126 Z= 0.131 Angle : 0.500 6.319 5623 Z= 0.244 Chirality : 0.043 0.274 635 Planarity : 0.004 0.039 703 Dihedral : 7.450 60.096 600 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.73 % Allowed : 12.41 % Favored : 86.86 % 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: 0.68 (0.38), residues: 506 helix: 1.43 (0.35), residues: 251 sheet: 0.13 (0.65), residues: 54 loop : -0.67 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.010 0.001 PHE A 174 TYR 0.006 0.001 TYR A 31 ARG 0.002 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.468 Fit side-chains REVERT: A 82 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5984 (p90) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.6912 time to fit residues: 29.7481 Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.128132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114585 restraints weight = 4885.893| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.37 r_work: 0.3268 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4126 Z= 0.168 Angle : 0.515 6.181 5623 Z= 0.250 Chirality : 0.044 0.265 635 Planarity : 0.004 0.038 703 Dihedral : 7.396 57.299 600 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.73 % Allowed : 12.65 % Favored : 86.62 % 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: 0.62 (0.38), residues: 506 helix: 1.41 (0.34), residues: 255 sheet: 0.11 (0.65), residues: 54 loop : -0.78 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.000 0.000 HIS A 425 PHE 0.010 0.001 PHE A 174 TYR 0.005 0.001 TYR A 313 ARG 0.001 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.03 seconds wall clock time: 29 minutes 16.10 seconds (1756.10 seconds total)