Starting phenix.real_space_refine on Wed Mar 5 18:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tma_41382/03_2025/8tma_41382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tma_41382/03_2025/8tma_41382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tma_41382/03_2025/8tma_41382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tma_41382/03_2025/8tma_41382.map" model { file = "/net/cci-nas-00/data/ceres_data/8tma_41382/03_2025/8tma_41382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tma_41382/03_2025/8tma_41382.cif" } resolution = 3.2 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= 0.098 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 11 5.16 5 C 2083 2.51 5 N 539 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3254 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1407 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1015 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.79, per 1000 atoms: 1.16 Number of scatterers: 3254 At special positions: 0 Unit cell: (72.6, 86.9, 79.2, 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 11 16.00 O 621 8.00 N 539 7.00 C 2083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 383.5 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.2% alpha, 38.3% 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 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.490A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.415A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.754A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.606A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.814A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 35 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 35B" --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.628A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 12.317A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.512A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.512A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 252 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: 0.88 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: 1026 1.34 - 1.46: 933 1.46 - 1.58: 1376 1.58 - 1.70: 0 1.70 - 1.82: 13 Bond restraints: 3348 Sorted by residual: bond pdb=" CG1 ILE A 434 " pdb=" CD1 ILE A 434 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.52e-01 bond pdb=" CB PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.49e-01 bond pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 1.460 1.473 -0.013 1.54e-02 4.22e+03 7.00e-01 bond pdb=" CG LEU H 20 " pdb=" CD1 LEU H 20 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.93e-01 bond pdb=" SD MET L 4 " pdb=" CE MET L 4 " ideal model delta sigma weight residual 1.791 1.773 0.018 2.50e-02 1.60e+03 5.39e-01 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 4342 1.48 - 2.95: 186 2.95 - 4.43: 22 4.43 - 5.91: 6 5.91 - 7.39: 1 Bond angle restraints: 4557 Sorted by residual: angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 105.31 7.39 3.00e+00 1.11e-01 6.06e+00 angle pdb=" C ASN H 64 " pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 122.46 125.80 -3.34 1.41e+00 5.03e-01 5.60e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 angle pdb=" CA CYS H 22 " pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " ideal model delta sigma weight residual 114.40 119.03 -4.63 2.30e+00 1.89e-01 4.06e+00 angle pdb=" CA CYS L 88 " pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 114.40 118.60 -4.20 2.30e+00 1.89e-01 3.33e+00 ... (remaining 4552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1784 16.87 - 33.74: 135 33.74 - 50.61: 12 50.61 - 67.48: 5 67.48 - 84.35: 4 Dihedral angle restraints: 1940 sinusoidal: 752 harmonic: 1188 Sorted by residual: dihedral pdb=" CA GLN L 89 " pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sinusoidal sigma weight residual -60.00 -114.44 54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CG ARG H 100A" pdb=" CD ARG H 100A" pdb=" NE ARG H 100A" pdb=" CZ ARG H 100A" ideal model delta sinusoidal sigma weight residual -90.00 -128.39 38.39 2 1.50e+01 4.44e-03 8.23e+00 dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 135.68 44.32 3 1.50e+01 4.44e-03 7.97e+00 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 250 0.032 - 0.063: 160 0.063 - 0.095: 34 0.095 - 0.127: 24 0.127 - 0.158: 10 Chirality restraints: 478 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 475 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.320 9.50e-02 1.11e+02 1.45e-01 1.69e+01 pdb=" NE ARG A 408 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " 0.122 9.50e-02 1.11e+02 5.51e-02 2.31e+00 pdb=" NE ARG A 466 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 100A" 0.108 9.50e-02 1.11e+02 4.89e-02 1.95e+00 pdb=" NE ARG H 100A" -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG H 100A" 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 100A" -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 100A" -0.000 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1109 2.84 - 3.35: 2644 3.35 - 3.87: 4739 3.87 - 4.38: 5348 4.38 - 4.90: 10154 Nonbonded interactions: 23994 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.324 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.328 3.120 nonbonded pdb=" OG SER L 14 " pdb=" OD2 ASP L 17 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.380 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OD1 ASN A 394 " model vdw 2.394 3.120 ... (remaining 23989 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 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: 3.220 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.800 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 0.043 3348 Z= 0.228 Angle : 0.682 7.387 4557 Z= 0.360 Chirality : 0.048 0.158 478 Planarity : 0.008 0.145 587 Dihedral : 12.057 84.349 1176 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.98 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -1.56 (0.39), residues: 402 helix: -4.09 (0.60), residues: 25 sheet: 0.34 (0.49), residues: 124 loop : -1.49 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 96 HIS 0.002 0.001 HIS H 40 PHE 0.018 0.002 PHE H 29 TYR 0.020 0.003 TYR H 91 ARG 0.036 0.003 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.6060 (Cg_endo) cc_final: 0.5845 (Cg_exo) REVERT: L 90 GLN cc_start: 0.8353 (pp30) cc_final: 0.7946 (pp30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1713 time to fit residues: 18.9868 Evaluate side-chains 58 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN H 6 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111887 restraints weight = 5073.108| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.39 r_work: 0.3244 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3348 Z= 0.397 Angle : 0.748 6.423 4557 Z= 0.395 Chirality : 0.051 0.169 478 Planarity : 0.005 0.034 587 Dihedral : 5.600 53.015 456 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 7.34 % Favored : 90.68 % 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: -1.27 (0.40), residues: 402 helix: -4.05 (0.57), residues: 25 sheet: 0.70 (0.47), residues: 134 loop : -1.46 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 96 HIS 0.004 0.002 HIS H 101 PHE 0.022 0.003 PHE H 29 TYR 0.021 0.002 TYR H 91 ARG 0.003 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.5826 (Cg_endo) cc_final: 0.5610 (Cg_exo) REVERT: L 107 LYS cc_start: 0.4942 (ttmt) cc_final: 0.4710 (tptp) outliers start: 7 outliers final: 7 residues processed: 63 average time/residue: 0.1719 time to fit residues: 13.0048 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114935 restraints weight = 5072.811| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.08 r_work: 0.3274 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.163 Angle : 0.564 5.599 4557 Z= 0.297 Chirality : 0.045 0.150 478 Planarity : 0.004 0.031 587 Dihedral : 4.923 49.649 456 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.26 % Allowed : 8.76 % Favored : 88.98 % 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: -0.89 (0.41), residues: 402 helix: -3.13 (0.71), residues: 31 sheet: 0.62 (0.46), residues: 144 loop : -1.04 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS H 40 PHE 0.010 0.001 PHE A 377 TYR 0.011 0.001 TYR H 91 ARG 0.001 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.5659 (Cg_endo) cc_final: 0.5431 (Cg_exo) REVERT: L 107 LYS cc_start: 0.5224 (ttmt) cc_final: 0.4848 (tptp) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.1721 time to fit residues: 13.0681 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.134839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113278 restraints weight = 5093.442| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.07 r_work: 0.3263 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.213 Angle : 0.574 5.219 4557 Z= 0.303 Chirality : 0.045 0.144 478 Planarity : 0.004 0.029 587 Dihedral : 4.788 44.535 456 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 9.04 % Favored : 87.85 % 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: -0.68 (0.41), residues: 402 helix: -3.61 (0.77), residues: 25 sheet: 0.86 (0.44), residues: 150 loop : -1.01 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.010 0.001 PHE H 53 TYR 0.013 0.002 TYR H 91 ARG 0.007 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7997 (ttp80) REVERT: H 14 PRO cc_start: 0.5713 (Cg_endo) cc_final: 0.5502 (Cg_exo) REVERT: L 107 LYS cc_start: 0.5411 (ttmt) cc_final: 0.5036 (tptp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.1529 time to fit residues: 12.2240 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.134348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113007 restraints weight = 5127.689| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.05 r_work: 0.3249 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3348 Z= 0.204 Angle : 0.561 5.254 4557 Z= 0.295 Chirality : 0.044 0.151 478 Planarity : 0.004 0.029 587 Dihedral : 4.565 36.857 456 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.82 % Allowed : 11.30 % Favored : 85.88 % 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: -0.64 (0.41), residues: 402 helix: -3.52 (0.82), residues: 25 sheet: 0.60 (0.44), residues: 155 loop : -0.78 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.009 0.001 PHE A 377 TYR 0.014 0.001 TYR H 91 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.338 Fit side-chains REVERT: L 107 LYS cc_start: 0.5505 (ttmt) cc_final: 0.5263 (tptp) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.1528 time to fit residues: 11.4072 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.134415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112846 restraints weight = 5244.517| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.08 r_work: 0.3266 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3348 Z= 0.192 Angle : 0.547 5.419 4557 Z= 0.289 Chirality : 0.044 0.154 478 Planarity : 0.004 0.031 587 Dihedral : 4.425 34.793 456 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.82 % Allowed : 12.43 % Favored : 84.75 % 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: -0.55 (0.41), residues: 402 helix: -3.53 (0.81), residues: 25 sheet: 0.68 (0.44), residues: 155 loop : -0.73 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.013 0.001 TYR H 91 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.369 Fit side-chains REVERT: A 403 ARG cc_start: 0.8517 (ttp80) cc_final: 0.7954 (ttp80) REVERT: L 107 LYS cc_start: 0.5370 (ttmt) cc_final: 0.5147 (tptp) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.1643 time to fit residues: 12.2712 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.133117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111779 restraints weight = 5089.952| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.04 r_work: 0.3245 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3348 Z= 0.229 Angle : 0.587 5.778 4557 Z= 0.307 Chirality : 0.045 0.153 478 Planarity : 0.004 0.028 587 Dihedral : 4.530 33.922 456 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.95 % Allowed : 11.30 % Favored : 84.75 % 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: -0.52 (0.41), residues: 402 helix: -3.47 (0.85), residues: 25 sheet: 0.68 (0.44), residues: 155 loop : -0.69 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 PHE 0.010 0.001 PHE H 53 TYR 0.015 0.002 TYR H 91 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.334 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 63 average time/residue: 0.1553 time to fit residues: 11.9659 Evaluate side-chains 62 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109361 restraints weight = 5098.034| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.07 r_work: 0.3205 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3348 Z= 0.324 Angle : 0.654 7.661 4557 Z= 0.343 Chirality : 0.047 0.179 478 Planarity : 0.004 0.030 587 Dihedral : 5.061 38.472 456 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.67 % Allowed : 11.02 % Favored : 85.31 % 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: -0.77 (0.41), residues: 402 helix: -3.58 (0.83), residues: 25 sheet: 0.53 (0.44), residues: 155 loop : -0.90 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS H 101 PHE 0.013 0.002 PHE H 29 TYR 0.017 0.002 TYR H 91 ARG 0.007 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.411 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 0.1586 time to fit residues: 12.1198 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.132704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111278 restraints weight = 5126.183| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.08 r_work: 0.3231 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3348 Z= 0.224 Angle : 0.599 8.620 4557 Z= 0.310 Chirality : 0.044 0.162 478 Planarity : 0.004 0.033 587 Dihedral : 4.771 37.374 456 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 11.86 % Favored : 85.03 % 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: -0.73 (0.41), residues: 402 helix: -3.55 (0.81), residues: 25 sheet: 0.58 (0.44), residues: 158 loop : -0.90 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.014 0.001 TYR H 91 ARG 0.008 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.366 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 59 average time/residue: 0.1599 time to fit residues: 11.5514 Evaluate side-chains 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.0030 overall best weight: 0.1306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116502 restraints weight = 5134.759| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.04 r_work: 0.3307 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3348 Z= 0.120 Angle : 0.488 5.423 4557 Z= 0.255 Chirality : 0.042 0.155 478 Planarity : 0.004 0.031 587 Dihedral : 4.068 29.195 456 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 12.43 % Favored : 85.59 % 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: -0.47 (0.41), residues: 402 helix: -2.89 (0.78), residues: 31 sheet: 0.76 (0.45), residues: 158 loop : -0.71 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.004 0.001 PHE H 53 TYR 0.008 0.001 TYR A 369 ARG 0.006 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.368 Fit side-chains REVERT: H 102 ILE cc_start: 0.8609 (mm) cc_final: 0.8334 (tt) REVERT: L 18 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5550 (ttt90) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1763 time to fit residues: 12.7839 Evaluate side-chains 59 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113444 restraints weight = 5154.330| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.02 r_work: 0.3265 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3348 Z= 0.225 Angle : 0.602 9.927 4557 Z= 0.310 Chirality : 0.044 0.157 478 Planarity : 0.004 0.029 587 Dihedral : 4.436 33.619 456 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.54 % Allowed : 12.15 % Favored : 85.31 % 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: -0.54 (0.41), residues: 402 helix: -3.58 (0.77), residues: 25 sheet: 0.77 (0.45), residues: 158 loop : -0.80 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 PHE 0.010 0.001 PHE H 53 TYR 0.015 0.001 TYR H 91 ARG 0.006 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.38 seconds wall clock time: 42 minutes 8.29 seconds (2528.29 seconds total)