Starting phenix.real_space_refine on Wed Mar 5 19:15:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3s_35155/03_2025/8i3s_35155.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3s_35155/03_2025/8i3s_35155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3s_35155/03_2025/8i3s_35155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3s_35155/03_2025/8i3s_35155.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3s_35155/03_2025/8i3s_35155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3s_35155/03_2025/8i3s_35155.cif" } resolution = 3.9 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= -0.003 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2074 2.51 5 N 554 2.21 5 O 628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3272 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.15, per 1000 atoms: 1.27 Number of scatterers: 3272 At special positions: 0 Unit cell: (67.45, 68.4, 96.9, 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 16 16.00 O 628 8.00 N 554 7.00 C 2074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.56 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 494.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.873A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.658A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.542A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.000A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.189A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.679A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 13 removed outlier: 7.060A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.670A pdb=" N ARG H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 52 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 46 82 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 679 1.45 - 1.57: 1787 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3349 Sorted by residual: bond pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 1.468 1.440 0.027 7.90e-03 1.60e+04 1.21e+01 bond pdb=" N ASN H 32 " pdb=" CA ASN H 32 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N PHE L 62 " pdb=" CA PHE L 62 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.49e+00 bond pdb=" N ILE L 58 " pdb=" CA ILE L 58 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" CA SER L 63 " pdb=" CB SER L 63 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.54e-02 4.22e+03 3.78e+00 ... (remaining 3344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 4343 1.17 - 2.34: 152 2.34 - 3.51: 38 3.51 - 4.68: 10 4.68 - 5.85: 4 Bond angle restraints: 4547 Sorted by residual: angle pdb=" CA ALA L 60 " pdb=" C ALA L 60 " pdb=" O ALA L 60 " ideal model delta sigma weight residual 120.81 116.22 4.59 1.15e+00 7.56e-01 1.60e+01 angle pdb=" N PRO L 59 " pdb=" CA PRO L 59 " pdb=" C PRO L 59 " ideal model delta sigma weight residual 113.12 107.27 5.85 1.65e+00 3.67e-01 1.26e+01 angle pdb=" CA PRO L 59 " pdb=" C PRO L 59 " pdb=" O PRO L 59 " ideal model delta sigma weight residual 121.38 118.69 2.69 7.70e-01 1.69e+00 1.22e+01 angle pdb=" C ILE H 31 " pdb=" N ASN H 32 " pdb=" CA ASN H 32 " ideal model delta sigma weight residual 122.87 117.62 5.25 1.61e+00 3.86e-01 1.06e+01 angle pdb=" N PRO L 59 " pdb=" CD PRO L 59 " pdb=" CG PRO L 59 " ideal model delta sigma weight residual 103.20 98.41 4.79 1.50e+00 4.44e-01 1.02e+01 ... (remaining 4542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 1779 12.35 - 24.70: 150 24.70 - 37.05: 50 37.05 - 49.40: 12 49.40 - 61.75: 9 Dihedral angle restraints: 2000 sinusoidal: 789 harmonic: 1211 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -114.61 28.61 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ARG L 61 " pdb=" CB ARG L 61 " pdb=" CG ARG L 61 " pdb=" CD ARG L 61 " ideal model delta sinusoidal sigma weight residual 180.00 123.29 56.71 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CA ILE A 434 " pdb=" CB ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CD1 ILE A 434 " ideal model delta sinusoidal sigma weight residual 60.00 115.51 -55.51 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 387 0.046 - 0.092: 74 0.092 - 0.138: 31 0.138 - 0.184: 4 0.184 - 0.230: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA PHE L 62 " pdb=" N PHE L 62 " pdb=" C PHE L 62 " pdb=" CB PHE L 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ALA L 60 " pdb=" N ALA L 60 " pdb=" C ALA L 60 " pdb=" CB ALA L 60 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 494 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 56 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C THR L 56 " 0.034 2.00e-02 2.50e+03 pdb=" O THR L 56 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 31 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C ILE H 31 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE H 31 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN H 32 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 101 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 102 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 102 " 0.023 5.00e-02 4.00e+02 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 560 2.77 - 3.30: 3130 3.30 - 3.83: 5250 3.83 - 4.37: 6115 4.37 - 4.90: 10669 Nonbonded interactions: 25724 Sorted by model distance: nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.242 3.040 nonbonded pdb=" NH2 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.301 3.120 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.340 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.369 3.040 ... (remaining 25719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3349 Z= 0.224 Angle : 0.587 5.846 4547 Z= 0.350 Chirality : 0.045 0.230 497 Planarity : 0.004 0.046 589 Dihedral : 11.402 61.753 1214 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.54 % Allowed : 11.02 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 414 helix: -2.41 (0.71), residues: 38 sheet: -0.53 (0.53), residues: 110 loop : -0.60 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.009 0.001 PHE A 515 TYR 0.010 0.001 TYR L 49 ARG 0.002 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8021 (t80) cc_final: 0.7522 (t80) REVERT: A 368 LEU cc_start: 0.5658 (mm) cc_final: 0.5449 (mm) REVERT: A 403 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8158 (ttp-110) REVERT: A 458 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8652 (mmtm) REVERT: A 507 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: H 10 GLU cc_start: 0.3299 (tt0) cc_final: 0.3026 (mt-10) REVERT: H 29 PHE cc_start: 0.7177 (m-80) cc_final: 0.6948 (m-10) REVERT: H 46 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7202 (mt-10) REVERT: H 79 TYR cc_start: 0.7709 (m-80) cc_final: 0.6961 (m-80) REVERT: L 4 MET cc_start: 0.7409 (mmm) cc_final: 0.6709 (mmm) REVERT: L 18 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.6999 (tpp-160) REVERT: L 36 TYR cc_start: 0.8654 (m-10) cc_final: 0.8420 (m-10) REVERT: L 49 TYR cc_start: 0.8499 (p90) cc_final: 0.8092 (p90) REVERT: L 87 TYR cc_start: 0.8368 (m-80) cc_final: 0.8127 (m-10) outliers start: 9 outliers final: 3 residues processed: 139 average time/residue: 0.2030 time to fit residues: 32.6576 Evaluate side-chains 105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 31 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124308 restraints weight = 6953.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127567 restraints weight = 4033.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129920 restraints weight = 2738.695| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3349 Z= 0.203 Angle : 0.573 5.292 4547 Z= 0.303 Chirality : 0.046 0.162 497 Planarity : 0.006 0.058 589 Dihedral : 4.705 39.162 490 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.80 % Allowed : 16.38 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.40), residues: 414 helix: -1.05 (0.91), residues: 31 sheet: -0.00 (0.54), residues: 97 loop : -0.77 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE A 464 TYR 0.013 0.001 TYR A 380 ARG 0.004 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7834 (ttt90) cc_final: 0.6861 (ttm170) REVERT: A 464 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6389 (t80) REVERT: A 474 GLN cc_start: 0.6367 (mt0) cc_final: 0.5890 (mm-40) REVERT: A 507 PRO cc_start: 0.8167 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: H 79 TYR cc_start: 0.7284 (m-80) cc_final: 0.6626 (m-80) REVERT: L 4 MET cc_start: 0.7505 (mmm) cc_final: 0.7142 (tpp) REVERT: L 11 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7085 (tm) REVERT: L 18 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.6983 (tpp-160) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 0.1924 time to fit residues: 25.2886 Evaluate side-chains 107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 6 GLN H 61 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.137729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121971 restraints weight = 7077.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125104 restraints weight = 4223.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127338 restraints weight = 2926.092| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3349 Z= 0.241 Angle : 0.594 6.561 4547 Z= 0.306 Chirality : 0.046 0.178 497 Planarity : 0.005 0.047 589 Dihedral : 4.882 41.027 488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.21 % Allowed : 18.36 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.95 (0.40), residues: 414 helix: -0.89 (0.97), residues: 31 sheet: -0.19 (0.52), residues: 96 loop : -0.76 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.015 0.001 PHE A 338 TYR 0.012 0.001 TYR H 47 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8261 (ttt90) cc_final: 0.6841 (ttm170) REVERT: A 464 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6063 (t80) REVERT: A 474 GLN cc_start: 0.6286 (mt0) cc_final: 0.5830 (mm-40) REVERT: H 79 TYR cc_start: 0.7248 (m-80) cc_final: 0.6652 (m-80) REVERT: L 4 MET cc_start: 0.7531 (mmm) cc_final: 0.6840 (mmm) REVERT: L 11 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7109 (tm) REVERT: L 18 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.6926 (tpp-160) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.1842 time to fit residues: 23.8115 Evaluate side-chains 106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.0020 chunk 12 optimal weight: 0.2980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 61 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124668 restraints weight = 6980.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127979 restraints weight = 4177.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130322 restraints weight = 2907.690| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3349 Z= 0.202 Angle : 0.572 5.489 4547 Z= 0.291 Chirality : 0.046 0.181 497 Planarity : 0.005 0.045 589 Dihedral : 4.782 40.086 488 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.78 % Allowed : 19.77 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 414 helix: -0.62 (1.14), residues: 25 sheet: -0.05 (0.52), residues: 94 loop : -0.67 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 103 HIS 0.000 0.000 HIS A 519 PHE 0.006 0.001 PHE A 464 TYR 0.014 0.001 TYR H 47 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.316 Fit side-chains REVERT: A 457 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7347 (ttt90) REVERT: A 464 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5972 (t80) REVERT: A 474 GLN cc_start: 0.6361 (mt0) cc_final: 0.5852 (mm-40) REVERT: H 29 PHE cc_start: 0.7061 (m-10) cc_final: 0.6534 (m-10) REVERT: H 79 TYR cc_start: 0.7247 (m-80) cc_final: 0.6627 (m-80) REVERT: H 86 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7198 (t70) REVERT: L 11 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7135 (tm) REVERT: L 18 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.6844 (tpp-160) outliers start: 24 outliers final: 14 residues processed: 110 average time/residue: 0.1587 time to fit residues: 20.9839 Evaluate side-chains 104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 61 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125243 restraints weight = 7058.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128565 restraints weight = 4236.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130971 restraints weight = 2952.896| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3349 Z= 0.198 Angle : 0.583 5.418 4547 Z= 0.297 Chirality : 0.046 0.178 497 Planarity : 0.005 0.043 589 Dihedral : 4.740 39.376 488 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.21 % Allowed : 21.19 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.83 (0.41), residues: 414 helix: -0.64 (1.13), residues: 25 sheet: -0.11 (0.51), residues: 88 loop : -0.69 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 103 HIS 0.000 0.000 HIS A 519 PHE 0.009 0.001 PHE A 338 TYR 0.012 0.001 TYR A 423 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7808 (t80) cc_final: 0.7409 (t80) REVERT: A 457 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7283 (ttt90) REVERT: H 79 TYR cc_start: 0.7259 (m-80) cc_final: 0.6646 (m-80) REVERT: L 11 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7120 (tm) REVERT: L 18 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.6829 (tpp-160) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 0.1575 time to fit residues: 20.2428 Evaluate side-chains 104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 chunk 37 optimal weight: 0.0000 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127378 restraints weight = 7064.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130669 restraints weight = 4206.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133012 restraints weight = 2918.139| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3349 Z= 0.182 Angle : 0.581 5.860 4547 Z= 0.295 Chirality : 0.046 0.176 497 Planarity : 0.004 0.041 589 Dihedral : 4.588 37.477 488 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 6.21 % Allowed : 21.19 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.76 (0.41), residues: 414 helix: -1.04 (1.09), residues: 27 sheet: 0.04 (0.51), residues: 97 loop : -0.65 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.014 0.001 PHE A 338 TYR 0.011 0.001 TYR H 47 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7051 (p0) cc_final: 0.6284 (t0) REVERT: A 457 ARG cc_start: 0.7686 (ttt-90) cc_final: 0.7438 (ttt90) REVERT: A 464 PHE cc_start: 0.6415 (t80) cc_final: 0.5899 (t80) REVERT: A 468 ILE cc_start: 0.9025 (pt) cc_final: 0.8783 (tt) REVERT: H 79 TYR cc_start: 0.7252 (m-80) cc_final: 0.6638 (m-80) REVERT: H 86 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6941 (t70) REVERT: L 4 MET cc_start: 0.6860 (tpp) cc_final: 0.6426 (tpp) REVERT: L 11 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7125 (tm) REVERT: L 18 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.6791 (tpp-160) outliers start: 22 outliers final: 14 residues processed: 111 average time/residue: 0.1869 time to fit residues: 24.4887 Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.138226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121519 restraints weight = 7028.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124639 restraints weight = 4287.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126848 restraints weight = 3023.167| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3349 Z= 0.341 Angle : 0.656 8.198 4547 Z= 0.344 Chirality : 0.048 0.204 497 Planarity : 0.005 0.045 589 Dihedral : 5.186 38.153 488 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.78 % Allowed : 23.16 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.04 (0.40), residues: 414 helix: -0.92 (1.02), residues: 26 sheet: -0.18 (0.49), residues: 101 loop : -0.88 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.002 PHE A 338 TYR 0.019 0.002 TYR H 90 ARG 0.004 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8304 (mtp180) REVERT: H 79 TYR cc_start: 0.7570 (m-80) cc_final: 0.6919 (m-80) REVERT: L 4 MET cc_start: 0.7068 (tpp) cc_final: 0.6093 (tpp) REVERT: L 11 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7392 (tm) REVERT: L 18 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7006 (tpp-160) REVERT: L 88 CYS cc_start: 0.7435 (t) cc_final: 0.6925 (t) outliers start: 24 outliers final: 20 residues processed: 101 average time/residue: 0.1668 time to fit residues: 20.1146 Evaluate side-chains 104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.141441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124537 restraints weight = 6990.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127762 restraints weight = 4222.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130067 restraints weight = 2961.449| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3349 Z= 0.228 Angle : 0.612 8.173 4547 Z= 0.317 Chirality : 0.047 0.217 497 Planarity : 0.005 0.073 589 Dihedral : 4.938 32.351 488 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.93 % Allowed : 25.14 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.08 (0.40), residues: 414 helix: -1.30 (1.00), residues: 27 sheet: -0.11 (0.50), residues: 101 loop : -0.90 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE A 338 TYR 0.013 0.001 TYR A 489 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7693 (t80) cc_final: 0.7222 (t80) REVERT: A 342 PHE cc_start: 0.7207 (m-10) cc_final: 0.6999 (m-10) REVERT: A 464 PHE cc_start: 0.6287 (t80) cc_final: 0.5780 (t80) REVERT: H 79 TYR cc_start: 0.7448 (m-80) cc_final: 0.6824 (m-80) REVERT: L 4 MET cc_start: 0.7098 (tpp) cc_final: 0.6673 (tpp) REVERT: L 11 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7413 (tm) REVERT: L 18 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.6861 (tpp-160) outliers start: 21 outliers final: 17 residues processed: 99 average time/residue: 0.1617 time to fit residues: 19.3214 Evaluate side-chains 98 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124701 restraints weight = 6972.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127961 restraints weight = 4195.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130312 restraints weight = 2928.819| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3349 Z= 0.225 Angle : 0.627 8.491 4547 Z= 0.322 Chirality : 0.047 0.199 497 Planarity : 0.005 0.063 589 Dihedral : 4.755 22.864 488 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.37 % Allowed : 26.27 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.07 (0.39), residues: 414 helix: -1.27 (0.99), residues: 27 sheet: -0.13 (0.51), residues: 95 loop : -0.88 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.014 0.001 PHE A 338 TYR 0.012 0.001 TYR A 489 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7694 (t80) cc_final: 0.7182 (t80) REVERT: A 342 PHE cc_start: 0.7088 (m-10) cc_final: 0.6838 (m-10) REVERT: A 394 ASN cc_start: 0.7292 (p0) cc_final: 0.6492 (t0) REVERT: A 464 PHE cc_start: 0.6243 (t80) cc_final: 0.5733 (t80) REVERT: H 79 TYR cc_start: 0.7313 (m-80) cc_final: 0.6747 (m-80) REVERT: L 4 MET cc_start: 0.7149 (tpp) cc_final: 0.6787 (tpp) REVERT: L 11 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7398 (tm) REVERT: L 18 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.6860 (tpp-160) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.1595 time to fit residues: 18.0573 Evaluate side-chains 94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123642 restraints weight = 6892.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126831 restraints weight = 4220.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129119 restraints weight = 2976.613| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3349 Z= 0.263 Angle : 0.637 8.900 4547 Z= 0.328 Chirality : 0.047 0.196 497 Planarity : 0.005 0.064 589 Dihedral : 4.815 19.591 487 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.37 % Allowed : 26.55 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.39), residues: 414 helix: -1.31 (0.99), residues: 27 sheet: -0.17 (0.51), residues: 95 loop : -0.94 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.013 0.001 PHE A 338 TYR 0.014 0.001 TYR A 489 ARG 0.003 0.000 ARG H 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7378 (p0) cc_final: 0.6683 (t0) REVERT: H 79 TYR cc_start: 0.7358 (m-80) cc_final: 0.6818 (m-80) REVERT: L 4 MET cc_start: 0.7316 (tpp) cc_final: 0.6967 (tpp) REVERT: L 11 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7455 (tm) REVERT: L 18 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.6960 (tpp-160) outliers start: 19 outliers final: 17 residues processed: 92 average time/residue: 0.1593 time to fit residues: 17.6335 Evaluate side-chains 95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124222 restraints weight = 6998.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127466 restraints weight = 4264.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129745 restraints weight = 2997.290| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3349 Z= 0.250 Angle : 0.648 8.918 4547 Z= 0.332 Chirality : 0.047 0.191 497 Planarity : 0.005 0.065 589 Dihedral : 4.821 19.617 487 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.80 % Allowed : 27.12 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.15 (0.39), residues: 414 helix: -1.43 (0.98), residues: 27 sheet: -0.14 (0.51), residues: 95 loop : -0.94 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.019 0.002 PHE A 338 TYR 0.013 0.001 TYR A 489 ARG 0.002 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.65 seconds wall clock time: 29 minutes 59.47 seconds (1799.47 seconds total)