Starting phenix.real_space_refine on Tue Jun 10 17:16:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wkw_32570/06_2025/7wkw_32570_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wkw_32570/06_2025/7wkw_32570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wkw_32570/06_2025/7wkw_32570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wkw_32570/06_2025/7wkw_32570.map" model { file = "/net/cci-nas-00/data/ceres_data/7wkw_32570/06_2025/7wkw_32570_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wkw_32570/06_2025/7wkw_32570_trim.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3938 2.51 5 N 940 2.21 5 O 998 1.98 5 H 6138 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12056 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "A" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.15, per 1000 atoms: 0.51 Number of scatterers: 12056 At special positions: 0 Unit cell: (80.845, 121.693, 71.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 998 8.00 N 940 7.00 C 3938 6.00 H 6138 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 80.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 3 through 30 removed outlier: 3.886A pdb=" N LEU B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.760A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.536A pdb=" N GLY B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 165 Processing helix chain 'B' and resid 167 through 171 removed outlier: 4.293A pdb=" N ALA B 170 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 Processing helix chain 'B' and resid 494 through 514 Processing helix chain 'B' and resid 518 through 530 removed outlier: 4.214A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 removed outlier: 3.514A pdb=" N GLN B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 581 removed outlier: 4.262A pdb=" N GLY B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 583 through 595 removed outlier: 4.004A pdb=" N ARG B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.837A pdb=" N PHE B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 640 removed outlier: 3.551A pdb=" N LEU B 616 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Proline residue: B 629 - end of helix Processing helix chain 'A' and resid 4 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 60 removed outlier: 4.811A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.764A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.542A pdb=" N GLY A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 165 Processing helix chain 'A' and resid 167 through 171 removed outlier: 4.268A pdb=" N ALA A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 Processing helix chain 'A' and resid 494 through 514 Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.208A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.512A pdb=" N GLN A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 581 removed outlier: 4.262A pdb=" N GLY A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 595 removed outlier: 3.978A pdb=" N ARG A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.845A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 640 removed outlier: 3.550A pdb=" N LEU A 616 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 174 through 177 removed outlier: 6.225A pdb=" N SER B 174 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 206 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS B 176 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 208 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 177 removed outlier: 6.229A pdb=" N SER A 174 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 206 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS A 176 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS A 208 " --> pdb=" O LYS A 176 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1323 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: 5.49 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6132 1.02 - 1.21: 8 1.21 - 1.41: 2426 1.41 - 1.61: 3560 1.61 - 1.81: 78 Bond restraints: 12204 Sorted by residual: bond pdb=" ND2 ASN A 112 " pdb="HD22 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN A 112 " pdb="HD21 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 112 " pdb="HD21 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN B 112 " pdb="HD22 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C12 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 1.347 1.458 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 12199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 21409 1.33 - 2.65: 685 2.65 - 3.98: 48 3.98 - 5.30: 10 5.30 - 6.63: 8 Bond angle restraints: 22160 Sorted by residual: angle pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 108.41 102.31 6.10 1.61e+00 3.86e-01 1.43e+01 angle pdb=" N ASN A 112 " pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 108.41 102.38 6.03 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 113.71 111.37 2.34 9.50e-01 1.11e+00 6.09e+00 angle pdb=" N VAL B 173 " pdb=" CA VAL B 173 " pdb=" C VAL B 173 " ideal model delta sigma weight residual 113.71 111.40 2.31 9.50e-01 1.11e+00 5.91e+00 angle pdb=" N TYR A 145 " pdb=" CA TYR A 145 " pdb=" C TYR A 145 " ideal model delta sigma weight residual 111.36 108.85 2.51 1.09e+00 8.42e-01 5.31e+00 ... (remaining 22155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5150 16.79 - 33.58: 403 33.58 - 50.37: 101 50.37 - 67.15: 54 67.15 - 83.94: 2 Dihedral angle restraints: 5710 sinusoidal: 3066 harmonic: 2644 Sorted by residual: dihedral pdb=" CA PHE A 49 " pdb=" C PHE A 49 " pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE B 49 " pdb=" C PHE B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 29 " pdb=" CD ARG B 29 " pdb=" NE ARG B 29 " pdb=" CZ ARG B 29 " ideal model delta sinusoidal sigma weight residual -180.00 -135.46 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 765 0.038 - 0.076: 165 0.076 - 0.115: 54 0.115 - 0.153: 4 0.153 - 0.191: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ASN B 112 " pdb=" N ASN B 112 " pdb=" C ASN B 112 " pdb=" CB ASN B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA ASN A 112 " pdb=" N ASN A 112 " pdb=" C ASN A 112 " pdb=" CB ASN A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA PRO A 16 " pdb=" N PRO A 16 " pdb=" C PRO A 16 " pdb=" CB PRO A 16 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 987 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 112 " -0.080 2.00e-02 2.50e+03 7.86e-02 9.27e+01 pdb=" CG ASN B 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 112 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN B 112 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 112 " 0.110 2.00e-02 2.50e+03 pdb="HD22 ASN B 112 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 112 " -0.077 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CG ASN A 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 112 " 0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN A 112 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 112 " 0.106 2.00e-02 2.50e+03 pdb="HD22 ASN A 112 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 569 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO B 570 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " -0.027 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 638 2.21 - 2.80: 24683 2.80 - 3.40: 33104 3.40 - 4.00: 42849 4.00 - 4.60: 67373 Nonbonded interactions: 168647 Sorted by model distance: nonbonded pdb=" O GLU B 178 " pdb="HH12 ARG B 489 " model vdw 1.607 2.450 nonbonded pdb=" HH TYR A 18 " pdb=" O MET A 624 " model vdw 1.607 2.450 nonbonded pdb=" O GLU A 178 " pdb="HH12 ARG A 489 " model vdw 1.608 2.450 nonbonded pdb=" HH TYR B 18 " pdb=" O MET B 624 " model vdw 1.609 2.450 nonbonded pdb=" O LEU B 23 " pdb=" HG SER B 27 " model vdw 1.615 2.450 ... (remaining 168642 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 39.110 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: 0.190 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:59.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 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 0.111 6066 Z= 0.197 Angle : 0.565 6.626 8266 Z= 0.297 Chirality : 0.038 0.191 990 Planarity : 0.005 0.048 998 Dihedral : 13.100 83.944 2134 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 746 helix: 1.70 (0.22), residues: 560 sheet: -0.12 (0.79), residues: 42 loop : -0.65 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.002 0.001 HIS B 57 PHE 0.007 0.001 PHE A 45 TYR 0.005 0.001 TYR B 635 ARG 0.002 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.10268 ( 443) hydrogen bonds : angle 6.00124 ( 1323) covalent geometry : bond 0.00392 ( 6066) covalent geometry : angle 0.56536 ( 8266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 2.0550 time to fit residues: 279.4944 Evaluate side-chains 84 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0040 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN A 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152396 restraints weight = 17339.186| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.45 r_work: 0.3529 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6066 Z= 0.203 Angle : 0.647 6.259 8266 Z= 0.330 Chirality : 0.040 0.126 990 Planarity : 0.006 0.075 998 Dihedral : 4.800 19.072 816 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 7.68 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 746 helix: 1.62 (0.22), residues: 566 sheet: 0.16 (0.80), residues: 42 loop : -0.86 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 506 HIS 0.003 0.001 HIS A 57 PHE 0.010 0.001 PHE B 56 TYR 0.011 0.002 TYR A 18 ARG 0.004 0.001 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 443) hydrogen bonds : angle 5.20532 ( 1323) covalent geometry : bond 0.00399 ( 6066) covalent geometry : angle 0.64705 ( 8266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6721 (ttp) cc_final: 0.6486 (ttp) REVERT: B 159 MET cc_start: 0.6780 (mtp) cc_final: 0.6442 (mtp) REVERT: A 21 MET cc_start: 0.6775 (ttp) cc_final: 0.6439 (ttp) REVERT: A 159 MET cc_start: 0.6784 (mtp) cc_final: 0.6466 (mtp) REVERT: A 162 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5296 (mtp) REVERT: A 624 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6466 (tpt) outliers start: 14 outliers final: 5 residues processed: 98 average time/residue: 1.8020 time to fit residues: 190.6180 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153219 restraints weight = 17652.740| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.17 r_work: 0.3534 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6066 Z= 0.202 Angle : 0.638 5.871 8266 Z= 0.333 Chirality : 0.044 0.258 990 Planarity : 0.005 0.049 998 Dihedral : 5.286 22.107 816 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.82 % Allowed : 8.78 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 746 helix: 1.52 (0.21), residues: 566 sheet: 0.02 (0.74), residues: 42 loop : -1.41 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 506 HIS 0.004 0.001 HIS B 57 PHE 0.013 0.002 PHE B 152 TYR 0.009 0.001 TYR B 498 ARG 0.004 0.001 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.05748 ( 443) hydrogen bonds : angle 5.22656 ( 1323) covalent geometry : bond 0.00406 ( 6066) covalent geometry : angle 0.63753 ( 8266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.7193 (mmm) cc_final: 0.6934 (tpp) REVERT: B 124 MET cc_start: 0.8108 (mtt) cc_final: 0.7876 (mtt) REVERT: B 624 MET cc_start: 0.7702 (tpp) cc_final: 0.6703 (tpt) REVERT: A 124 MET cc_start: 0.8153 (mtt) cc_final: 0.7938 (mtt) outliers start: 18 outliers final: 5 residues processed: 104 average time/residue: 2.5476 time to fit residues: 284.4164 Evaluate side-chains 82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 585 ASP Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 63 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.181975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153151 restraints weight = 17587.881| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.16 r_work: 0.3602 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6066 Z= 0.152 Angle : 0.562 5.936 8266 Z= 0.292 Chirality : 0.039 0.186 990 Planarity : 0.005 0.047 998 Dihedral : 4.930 23.062 816 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.72 % Allowed : 10.97 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.31), residues: 746 helix: 1.63 (0.22), residues: 568 sheet: 0.03 (0.75), residues: 42 loop : -1.16 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.003 0.001 HIS A 57 PHE 0.008 0.001 PHE A 45 TYR 0.005 0.001 TYR A 609 ARG 0.004 0.001 ARG B 489 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 443) hydrogen bonds : angle 4.94509 ( 1323) covalent geometry : bond 0.00329 ( 6066) covalent geometry : angle 0.56231 ( 8266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 624 MET cc_start: 0.7910 (tpp) cc_final: 0.6778 (tpt) REVERT: A 585 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6924 (t0) REVERT: A 624 MET cc_start: 0.7884 (tpt) cc_final: 0.6737 (tpt) outliers start: 11 outliers final: 5 residues processed: 92 average time/residue: 1.8651 time to fit residues: 182.9870 Evaluate side-chains 80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.181545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152589 restraints weight = 17596.430| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.15 r_work: 0.3620 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6066 Z= 0.122 Angle : 0.518 6.681 8266 Z= 0.264 Chirality : 0.037 0.136 990 Planarity : 0.005 0.043 998 Dihedral : 4.464 17.275 816 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.88 % Allowed : 11.13 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.32), residues: 746 helix: 1.82 (0.22), residues: 568 sheet: 0.04 (0.74), residues: 42 loop : -1.04 (0.61), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.002 0.001 HIS B 57 PHE 0.008 0.001 PHE B 603 TYR 0.006 0.001 TYR B 635 ARG 0.002 0.000 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 443) hydrogen bonds : angle 4.82103 ( 1323) covalent geometry : bond 0.00245 ( 6066) covalent geometry : angle 0.51783 ( 8266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 624 MET cc_start: 0.7894 (tpp) cc_final: 0.7028 (tpt) REVERT: A 585 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6934 (t0) REVERT: A 624 MET cc_start: 0.7892 (tpt) cc_final: 0.6735 (tpt) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 1.8870 time to fit residues: 161.1625 Evaluate side-chains 80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 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 = 0.3978 r_free = 0.3978 target = 0.175547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145897 restraints weight = 17889.014| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.17 r_work: 0.3462 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.7828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6066 Z= 0.211 Angle : 0.663 6.245 8266 Z= 0.352 Chirality : 0.043 0.153 990 Planarity : 0.006 0.054 998 Dihedral : 6.209 40.459 816 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.19 % Allowed : 10.50 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 746 helix: 1.29 (0.21), residues: 564 sheet: 0.08 (0.73), residues: 42 loop : -1.55 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 506 HIS 0.005 0.001 HIS B 187 PHE 0.011 0.002 PHE A 605 TYR 0.010 0.002 TYR B 498 ARG 0.005 0.001 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.05917 ( 443) hydrogen bonds : angle 5.28799 ( 1323) covalent geometry : bond 0.00482 ( 6066) covalent geometry : angle 0.66309 ( 8266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8565 (ttp) cc_final: 0.8353 (ttt) REVERT: B 178 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: B 624 MET cc_start: 0.8175 (tpp) cc_final: 0.7151 (tpt) REVERT: A 21 MET cc_start: 0.8570 (ttp) cc_final: 0.8352 (ttt) REVERT: A 178 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6647 (mp0) outliers start: 14 outliers final: 6 residues processed: 98 average time/residue: 2.0738 time to fit residues: 215.5945 Evaluate side-chains 83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147274 restraints weight = 17714.102| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.19 r_work: 0.3553 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6066 Z= 0.127 Angle : 0.546 8.648 8266 Z= 0.285 Chirality : 0.037 0.131 990 Planarity : 0.005 0.050 998 Dihedral : 4.957 23.405 816 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 13.01 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.31), residues: 746 helix: 1.56 (0.21), residues: 568 sheet: -0.01 (0.74), residues: 42 loop : -1.16 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.001 HIS A 57 PHE 0.008 0.001 PHE B 566 TYR 0.010 0.001 TYR A 635 ARG 0.002 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 443) hydrogen bonds : angle 5.00216 ( 1323) covalent geometry : bond 0.00263 ( 6066) covalent geometry : angle 0.54649 ( 8266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.960 Fit side-chains REVERT: B 21 MET cc_start: 0.8499 (ttp) cc_final: 0.7994 (ttt) REVERT: B 178 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: B 624 MET cc_start: 0.8104 (tpp) cc_final: 0.7008 (tpt) REVERT: A 21 MET cc_start: 0.8471 (ttp) cc_final: 0.8080 (ttt) REVERT: A 127 GLU cc_start: 0.6571 (mp0) cc_final: 0.6322 (mm-30) REVERT: A 624 MET cc_start: 0.8152 (tpt) cc_final: 0.7026 (tpt) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 2.1901 time to fit residues: 193.3606 Evaluate side-chains 82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.173653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144052 restraints weight = 17809.147| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.16 r_work: 0.3503 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.8401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6066 Z= 0.181 Angle : 0.618 8.912 8266 Z= 0.324 Chirality : 0.039 0.140 990 Planarity : 0.006 0.054 998 Dihedral : 5.555 32.714 816 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.19 % Allowed : 13.01 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 746 helix: 1.41 (0.21), residues: 564 sheet: -0.06 (0.72), residues: 42 loop : -1.47 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 506 HIS 0.003 0.001 HIS B 187 PHE 0.008 0.002 PHE B 566 TYR 0.009 0.001 TYR A 498 ARG 0.003 0.001 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.05286 ( 443) hydrogen bonds : angle 5.18449 ( 1323) covalent geometry : bond 0.00414 ( 6066) covalent geometry : angle 0.61752 ( 8266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8544 (ttp) cc_final: 0.8342 (ttt) REVERT: B 127 GLU cc_start: 0.6819 (mp0) cc_final: 0.6591 (mm-30) REVERT: B 178 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: B 520 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7089 (mt) REVERT: B 624 MET cc_start: 0.8225 (tpp) cc_final: 0.7287 (tpt) REVERT: A 21 MET cc_start: 0.8519 (ttp) cc_final: 0.8264 (ttt) REVERT: A 127 GLU cc_start: 0.6790 (mp0) cc_final: 0.6466 (mm-30) REVERT: A 624 MET cc_start: 0.8250 (tpt) cc_final: 0.6864 (tpt) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 2.1952 time to fit residues: 206.7066 Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145907 restraints weight = 17626.527| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.16 r_work: 0.3527 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.8563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6066 Z= 0.145 Angle : 0.572 9.853 8266 Z= 0.296 Chirality : 0.038 0.133 990 Planarity : 0.005 0.052 998 Dihedral : 5.066 26.040 816 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.88 % Allowed : 13.64 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.30), residues: 746 helix: 1.47 (0.21), residues: 568 sheet: -0.02 (0.74), residues: 42 loop : -1.25 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.002 0.001 HIS A 187 PHE 0.008 0.001 PHE B 566 TYR 0.009 0.001 TYR A 635 ARG 0.002 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 443) hydrogen bonds : angle 5.06395 ( 1323) covalent geometry : bond 0.00320 ( 6066) covalent geometry : angle 0.57164 ( 8266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8534 (ttp) cc_final: 0.8055 (ttt) REVERT: B 127 GLU cc_start: 0.6718 (mp0) cc_final: 0.6416 (mm-30) REVERT: B 178 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: B 624 MET cc_start: 0.8203 (tpp) cc_final: 0.7229 (tpt) REVERT: A 21 MET cc_start: 0.8520 (ttp) cc_final: 0.8272 (ttt) REVERT: A 127 GLU cc_start: 0.6688 (mp0) cc_final: 0.6421 (mm-30) REVERT: A 472 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.6364 (t0) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 2.2694 time to fit residues: 225.0630 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 19 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.174581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145684 restraints weight = 17668.670| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.16 r_work: 0.3492 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.8760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6066 Z= 0.171 Angle : 0.600 9.499 8266 Z= 0.311 Chirality : 0.039 0.137 990 Planarity : 0.006 0.053 998 Dihedral : 5.428 31.270 816 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.88 % Allowed : 13.17 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 746 helix: 1.41 (0.21), residues: 564 sheet: -0.09 (0.74), residues: 42 loop : -1.44 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 506 HIS 0.002 0.001 HIS A 187 PHE 0.009 0.002 PHE A 45 TYR 0.010 0.001 TYR A 635 ARG 0.003 0.001 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 443) hydrogen bonds : angle 5.16891 ( 1323) covalent geometry : bond 0.00392 ( 6066) covalent geometry : angle 0.59953 ( 8266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: B 127 GLU cc_start: 0.6843 (mp0) cc_final: 0.6582 (mm-30) REVERT: B 178 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: B 624 MET cc_start: 0.8255 (tpp) cc_final: 0.7292 (tpt) REVERT: A 21 MET cc_start: 0.8562 (ttp) cc_final: 0.8028 (ttt) REVERT: A 127 GLU cc_start: 0.6812 (mp0) cc_final: 0.6541 (mm-30) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 2.2854 time to fit residues: 219.7221 Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145236 restraints weight = 17593.023| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.15 r_work: 0.3543 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.8821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6066 Z= 0.126 Angle : 0.548 8.772 8266 Z= 0.285 Chirality : 0.037 0.131 990 Planarity : 0.005 0.050 998 Dihedral : 4.785 21.142 816 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.41 % Allowed : 14.11 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.31), residues: 746 helix: 1.60 (0.21), residues: 568 sheet: -0.02 (0.75), residues: 42 loop : -1.21 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 144 HIS 0.002 0.001 HIS A 57 PHE 0.007 0.001 PHE A 566 TYR 0.009 0.001 TYR B 635 ARG 0.002 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 443) hydrogen bonds : angle 4.98381 ( 1323) covalent geometry : bond 0.00270 ( 6066) covalent geometry : angle 0.54836 ( 8266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9436.83 seconds wall clock time: 164 minutes 13.67 seconds (9853.67 seconds total)