Starting phenix.real_space_refine on Thu Jul 18 22:51:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yni_33962/07_2024/7yni_33962.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yni_33962/07_2024/7yni_33962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yni_33962/07_2024/7yni_33962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yni_33962/07_2024/7yni_33962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yni_33962/07_2024/7yni_33962.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yni_33962/07_2024/7yni_33962.cif" } resolution = 3.26 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= 0.009 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 2926 2.51 5 N 694 2.21 5 O 734 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4387 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4182 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 21, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "B" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 193 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'KQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.75 Number of scatterers: 4387 At special positions: 0 Unit cell: (85.068, 75.06, 77.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 F 1 9.00 O 734 8.00 N 694 7.00 C 2926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 797.3 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 83.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 25 through 48 removed outlier: 3.594A pdb=" N ILE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.609A pdb=" N GLY A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 139 through 173 removed outlier: 4.477A pdb=" N ILE A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 201 through 227 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.017A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.837A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.506A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.696A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 375 through 409 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 445 Proline residue: A 442 - end of helix removed outlier: 3.641A pdb=" N GLN A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 481 through 507 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.729A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'B' and resid 28 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 355 hydrogen bonds defined for protein. 1059 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: 1.27 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1215 1.34 - 1.45: 776 1.45 - 1.57: 2452 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4494 Sorted by residual: bond pdb=" C1 KQC A 701 " pdb=" O1 KQC A 701 " ideal model delta sigma weight residual 1.375 1.432 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CA VAL A 441 " pdb=" C VAL A 441 " ideal model delta sigma weight residual 1.524 1.502 0.023 1.11e-02 8.12e+03 4.12e+00 bond pdb=" N VAL A 441 " pdb=" CA VAL A 441 " ideal model delta sigma weight residual 1.463 1.486 -0.023 1.18e-02 7.18e+03 3.85e+00 bond pdb=" CA TYR A 366 " pdb=" C TYR A 366 " ideal model delta sigma weight residual 1.520 1.500 0.021 1.23e-02 6.61e+03 2.80e+00 bond pdb=" C LEU A 387 " pdb=" O LEU A 387 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.17e-02 7.31e+03 2.48e+00 ... (remaining 4489 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.14: 133 107.14 - 113.97: 2657 113.97 - 120.80: 2114 120.80 - 127.63: 1188 127.63 - 134.46: 54 Bond angle restraints: 6146 Sorted by residual: angle pdb=" N ARG A 135 " pdb=" CA ARG A 135 " pdb=" C ARG A 135 " ideal model delta sigma weight residual 111.36 117.03 -5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N PRO A 552 " pdb=" CA PRO A 552 " pdb=" C PRO A 552 " ideal model delta sigma weight residual 112.47 118.72 -6.25 2.06e+00 2.36e-01 9.21e+00 angle pdb=" N VAL A 441 " pdb=" CA VAL A 441 " pdb=" CB VAL A 441 " ideal model delta sigma weight residual 110.52 108.56 1.96 6.70e-01 2.23e+00 8.58e+00 angle pdb=" CA TRP A 68 " pdb=" CB TRP A 68 " pdb=" CG TRP A 68 " ideal model delta sigma weight residual 113.60 119.11 -5.51 1.90e+00 2.77e-01 8.41e+00 angle pdb=" C ILE A 364 " pdb=" CA ILE A 364 " pdb=" CB ILE A 364 " ideal model delta sigma weight residual 112.19 109.29 2.90 1.15e+00 7.56e-01 6.37e+00 ... (remaining 6141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2427 15.76 - 31.52: 131 31.52 - 47.28: 32 47.28 - 63.04: 3 63.04 - 78.80: 3 Dihedral angle restraints: 2596 sinusoidal: 886 harmonic: 1710 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -135.79 49.79 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 133.53 -40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS A 345 " pdb=" SG CYS A 345 " pdb=" SG CYS A 351 " pdb=" CB CYS A 351 " ideal model delta sinusoidal sigma weight residual 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 2593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 540 0.039 - 0.078: 163 0.078 - 0.117: 47 0.117 - 0.156: 8 0.156 - 0.195: 3 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA PRO A 552 " pdb=" N PRO A 552 " pdb=" C PRO A 552 " pdb=" CB PRO A 552 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ARG A 135 " pdb=" N ARG A 135 " pdb=" C ARG A 135 " pdb=" CB ARG A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 758 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 154 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 154 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE A 154 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 155 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 155 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PHE A 155 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE A 155 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 551 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 552 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " -0.036 5.00e-02 4.00e+02 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 602 2.75 - 3.28: 4879 3.28 - 3.82: 7903 3.82 - 4.36: 8927 4.36 - 4.90: 15620 Nonbonded interactions: 37931 Sorted by model distance: nonbonded pdb=" NE2 HIS A 83 " pdb=" O1 KQC A 701 " model vdw 2.206 2.520 nonbonded pdb=" NE2 GLN A 207 " pdb=" CA ALA A 388 " model vdw 2.233 3.550 nonbonded pdb=" OH TYR A 35 " pdb=" NE2 GLN A 207 " model vdw 2.287 2.520 nonbonded pdb=" OH TYR A 557 " pdb=" OE1 GLU A 568 " model vdw 2.295 2.440 nonbonded pdb=" O GLN A 448 " pdb=" OG SER A 449 " model vdw 2.296 2.440 ... (remaining 37926 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: 0.760 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 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 : 0.004 0.057 4494 Z= 0.290 Angle : 0.661 7.378 6146 Z= 0.374 Chirality : 0.042 0.195 761 Planarity : 0.006 0.067 734 Dihedral : 10.917 78.797 1487 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.98 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.78 (0.35), residues: 582 helix: 1.18 (0.24), residues: 442 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 68 HIS 0.005 0.001 HIS A 83 PHE 0.011 0.002 PHE A 663 TYR 0.020 0.002 TYR A 144 ARG 0.009 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7696 (tpt) cc_final: 0.7003 (tpt) REVERT: A 328 MET cc_start: 0.7002 (mtt) cc_final: 0.5502 (mtt) REVERT: A 526 TYR cc_start: 0.6157 (p90) cc_final: 0.4766 (p90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1772 time to fit residues: 10.9570 Evaluate side-chains 43 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4494 Z= 0.295 Angle : 0.688 7.481 6146 Z= 0.359 Chirality : 0.046 0.209 761 Planarity : 0.006 0.062 734 Dihedral : 4.571 18.851 646 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.85 % Rotamer: Outliers : 0.70 % Allowed : 6.05 % Favored : 93.26 % 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: 0.93 (0.35), residues: 582 helix: 1.29 (0.24), residues: 447 sheet: None (None), residues: 0 loop : -1.60 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 30 HIS 0.005 0.001 HIS A 660 PHE 0.017 0.002 PHE A 232 TYR 0.013 0.002 TYR A 236 ARG 0.005 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.448 Fit side-chains REVERT: A 233 MET cc_start: 0.6691 (mtm) cc_final: 0.6454 (mtm) REVERT: A 300 ARG cc_start: 0.7079 (mpt180) cc_final: 0.6204 (mpt180) REVERT: A 328 MET cc_start: 0.6866 (mtt) cc_final: 0.5622 (mtt) REVERT: A 407 MET cc_start: 0.7068 (mtm) cc_final: 0.6860 (mtp) REVERT: A 632 MET cc_start: 0.7085 (tpp) cc_final: 0.6883 (mpp) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.1726 time to fit residues: 10.8230 Evaluate side-chains 43 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4494 Z= 0.232 Angle : 0.630 7.240 6146 Z= 0.329 Chirality : 0.043 0.218 761 Planarity : 0.006 0.059 734 Dihedral : 4.374 18.685 646 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.47 % Favored : 95.02 % Rotamer: Outliers : 0.93 % Allowed : 10.47 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 582 helix: 1.47 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.71 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 30 HIS 0.004 0.001 HIS A 660 PHE 0.015 0.001 PHE A 232 TYR 0.012 0.001 TYR A 236 ARG 0.003 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.417 Fit side-chains REVERT: A 233 MET cc_start: 0.6638 (mtm) cc_final: 0.6352 (mtm) REVERT: A 300 ARG cc_start: 0.7140 (mpt180) cc_final: 0.6521 (mpt180) REVERT: A 328 MET cc_start: 0.6933 (mtt) cc_final: 0.5568 (mtt) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.1566 time to fit residues: 9.3871 Evaluate side-chains 46 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4494 Z= 0.243 Angle : 0.611 7.255 6146 Z= 0.322 Chirality : 0.043 0.220 761 Planarity : 0.006 0.057 734 Dihedral : 4.276 18.106 646 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.50 % Favored : 93.99 % Rotamer: Outliers : 2.33 % Allowed : 11.86 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.36), residues: 582 helix: 1.55 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.87 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 30 HIS 0.003 0.001 HIS A 660 PHE 0.016 0.001 PHE A 232 TYR 0.011 0.001 TYR A 236 ARG 0.004 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.484 Fit side-chains REVERT: A 233 MET cc_start: 0.6684 (mtm) cc_final: 0.6425 (mtm) REVERT: A 300 ARG cc_start: 0.7114 (mpt180) cc_final: 0.6625 (mpt180) REVERT: A 325 MET cc_start: 0.7447 (ttt) cc_final: 0.7207 (ttt) REVERT: A 328 MET cc_start: 0.7137 (mtt) cc_final: 0.5811 (mtt) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.1491 time to fit residues: 10.7037 Evaluate side-chains 47 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 525 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4494 Z= 0.372 Angle : 0.714 8.941 6146 Z= 0.371 Chirality : 0.047 0.215 761 Planarity : 0.006 0.063 734 Dihedral : 4.464 18.669 646 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.67 % Favored : 93.81 % Rotamer: Outliers : 2.33 % Allowed : 15.12 % Favored : 82.56 % 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: 0.52 (0.35), residues: 582 helix: 1.05 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -2.04 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 30 HIS 0.006 0.002 HIS A 83 PHE 0.018 0.002 PHE A 232 TYR 0.013 0.002 TYR A 236 ARG 0.003 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.467 Fit side-chains REVERT: A 128 MET cc_start: 0.7365 (mmp) cc_final: 0.7037 (mmp) REVERT: A 210 ILE cc_start: 0.5574 (mt) cc_final: 0.5236 (mt) REVERT: A 233 MET cc_start: 0.6876 (mtm) cc_final: 0.6576 (mtm) REVERT: A 300 ARG cc_start: 0.7181 (mpt180) cc_final: 0.6578 (mpt180) REVERT: A 328 MET cc_start: 0.7260 (mtt) cc_final: 0.6247 (mtt) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1565 time to fit residues: 11.6575 Evaluate side-chains 55 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4494 Z= 0.243 Angle : 0.617 7.239 6146 Z= 0.325 Chirality : 0.042 0.216 761 Planarity : 0.006 0.058 734 Dihedral : 4.267 17.840 646 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Rotamer: Outliers : 2.56 % Allowed : 16.28 % Favored : 81.16 % 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: 0.99 (0.36), residues: 582 helix: 1.43 (0.25), residues: 448 sheet: None (None), residues: 0 loop : -2.02 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 30 HIS 0.003 0.001 HIS A 660 PHE 0.017 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.432 Fit side-chains REVERT: A 233 MET cc_start: 0.6753 (mtm) cc_final: 0.6448 (mtm) REVERT: A 300 ARG cc_start: 0.7142 (mpt180) cc_final: 0.6649 (mpt180) REVERT: A 328 MET cc_start: 0.7109 (mtt) cc_final: 0.5916 (mtt) REVERT: A 407 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6611 (mtm) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1543 time to fit residues: 10.0132 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4494 Z= 0.221 Angle : 0.606 7.470 6146 Z= 0.318 Chirality : 0.042 0.220 761 Planarity : 0.006 0.058 734 Dihedral : 4.205 17.283 646 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 2.79 % Allowed : 17.44 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.36), residues: 582 helix: 1.70 (0.25), residues: 443 sheet: None (None), residues: 0 loop : -1.85 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.002 0.001 HIS A 660 PHE 0.015 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.466 Fit side-chains REVERT: A 233 MET cc_start: 0.6660 (mtm) cc_final: 0.6360 (mtm) REVERT: A 283 MET cc_start: 0.7451 (tpt) cc_final: 0.7201 (tpt) REVERT: A 300 ARG cc_start: 0.7082 (mpt180) cc_final: 0.6673 (mpt180) REVERT: A 328 MET cc_start: 0.7087 (mtt) cc_final: 0.5937 (mtt) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.1658 time to fit residues: 11.2215 Evaluate side-chains 50 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6520 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4494 Z= 0.226 Angle : 0.615 8.805 6146 Z= 0.319 Chirality : 0.042 0.215 761 Planarity : 0.006 0.057 734 Dihedral : 4.181 16.972 646 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Rotamer: Outliers : 2.79 % Allowed : 17.21 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.36), residues: 582 helix: 1.64 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -2.02 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 30 HIS 0.002 0.001 HIS A 660 PHE 0.015 0.001 PHE A 232 TYR 0.009 0.001 TYR A 191 ARG 0.005 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.483 Fit side-chains REVERT: A 233 MET cc_start: 0.6666 (mtm) cc_final: 0.6365 (mtm) REVERT: A 300 ARG cc_start: 0.7058 (mpt180) cc_final: 0.6700 (mpt180) REVERT: A 328 MET cc_start: 0.7092 (mtt) cc_final: 0.6044 (mtt) REVERT: A 407 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6739 (mtp) outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.1706 time to fit residues: 11.7361 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0070 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4494 Z= 0.204 Angle : 0.595 8.400 6146 Z= 0.311 Chirality : 0.042 0.219 761 Planarity : 0.006 0.056 734 Dihedral : 4.132 18.257 646 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.98 % Favored : 94.50 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.36), residues: 582 helix: 1.88 (0.25), residues: 443 sheet: None (None), residues: 0 loop : -1.89 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 30 HIS 0.002 0.000 HIS A 660 PHE 0.014 0.001 PHE A 232 TYR 0.010 0.001 TYR A 191 ARG 0.006 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.429 Fit side-chains REVERT: A 233 MET cc_start: 0.6587 (mtm) cc_final: 0.6307 (mtm) REVERT: A 283 MET cc_start: 0.7722 (tpt) cc_final: 0.7471 (tpt) REVERT: A 300 ARG cc_start: 0.7052 (mpt180) cc_final: 0.6743 (mpt180) REVERT: A 328 MET cc_start: 0.7067 (mtt) cc_final: 0.6086 (mtt) REVERT: A 407 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6625 (mtp) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.1362 time to fit residues: 9.4159 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 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: 0.6513 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4494 Z= 0.229 Angle : 0.621 10.822 6146 Z= 0.321 Chirality : 0.042 0.217 761 Planarity : 0.006 0.057 734 Dihedral : 4.159 19.117 646 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 2.09 % Allowed : 18.37 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.36), residues: 582 helix: 1.72 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -2.08 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 30 HIS 0.002 0.001 HIS A 660 PHE 0.015 0.001 PHE A 232 TYR 0.009 0.001 TYR A 191 ARG 0.005 0.001 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.577 Fit side-chains REVERT: A 283 MET cc_start: 0.7745 (tpt) cc_final: 0.7400 (tpt) REVERT: A 300 ARG cc_start: 0.7060 (mpt180) cc_final: 0.6733 (mpt180) REVERT: A 328 MET cc_start: 0.7156 (mtt) cc_final: 0.6158 (mtt) REVERT: A 407 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6610 (mtm) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.1550 time to fit residues: 10.1731 Evaluate side-chains 50 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 52 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.193064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161177 restraints weight = 4216.750| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.84 r_work: 0.3844 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4494 Z= 0.200 Angle : 0.623 11.637 6146 Z= 0.320 Chirality : 0.041 0.216 761 Planarity : 0.006 0.056 734 Dihedral : 4.198 22.222 646 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.81 % Favored : 94.85 % Rotamer: Outliers : 2.09 % Allowed : 18.84 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.36), residues: 582 helix: 1.83 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -1.99 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 30 HIS 0.002 0.001 HIS A 660 PHE 0.013 0.001 PHE A 232 TYR 0.010 0.001 TYR A 191 ARG 0.005 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.81 seconds wall clock time: 23 minutes 30.21 seconds (1410.21 seconds total)