Starting phenix.real_space_refine on Thu Sep 26 02:36:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/09_2024/7wkw_32570_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/09_2024/7wkw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/09_2024/7wkw_32570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/09_2024/7wkw_32570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/09_2024/7wkw_32570_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/09_2024/7wkw_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-5461/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: 6.48, per 1000 atoms: 0.54 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: 3.82 Conformation dependent library (CDL) restraints added in 1.0 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: 0.94 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: 5.27 Time building geometry restraints manager: 4.23 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: 0.00 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: 1.300 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: 0.210 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- 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= 0.235 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.957 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: 1.9301 time to fit residues: 262.5528 Evaluate side-chains 84 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2738 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= 0.268 Angle : 0.647 6.259 8266 Z= 0.330 Chirality : 0.040 0.126 990 Planarity : 0.006 0.075 998 Dihedral : 4.800 19.083 816 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 *********************** 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 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6543 (ttp) cc_final: 0.6274 (ttp) REVERT: B 159 MET cc_start: 0.6480 (mtp) cc_final: 0.6170 (mtp) REVERT: A 21 MET cc_start: 0.6610 (ttp) cc_final: 0.6221 (ttp) REVERT: A 159 MET cc_start: 0.6477 (mtp) cc_final: 0.6177 (mtp) REVERT: A 162 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.4776 (mtp) REVERT: A 624 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.5932 (tpt) outliers start: 14 outliers final: 5 residues processed: 97 average time/residue: 1.6085 time to fit residues: 168.1226 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 37 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6066 Z= 0.292 Angle : 0.685 5.859 8266 Z= 0.356 Chirality : 0.045 0.263 990 Planarity : 0.006 0.052 998 Dihedral : 5.698 26.460 816 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.82 % Allowed : 9.56 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.31), residues: 746 helix: 1.35 (0.21), residues: 566 sheet: 0.07 (0.75), residues: 42 loop : -1.51 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 506 HIS 0.004 0.001 HIS B 57 PHE 0.015 0.002 PHE B 152 TYR 0.012 0.002 TYR B 498 ARG 0.004 0.001 ARG B 481 *********************** 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 118 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.6861 (mmm) cc_final: 0.6638 (tpp) REVERT: B 124 MET cc_start: 0.7931 (mtt) cc_final: 0.7718 (mtt) REVERT: B 585 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6587 (t0) REVERT: B 624 MET cc_start: 0.7573 (tpp) cc_final: 0.6178 (tpt) REVERT: A 124 MET cc_start: 0.7967 (mtt) cc_final: 0.7757 (mtt) REVERT: A 585 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6567 (t70) outliers start: 18 outliers final: 4 residues processed: 109 average time/residue: 1.7143 time to fit residues: 200.5371 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 585 ASP 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 66 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6303 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= 0.224 Angle : 0.587 4.995 8266 Z= 0.303 Chirality : 0.040 0.192 990 Planarity : 0.005 0.049 998 Dihedral : 5.144 26.967 816 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.72 % Allowed : 11.76 % Favored : 86.52 % 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: 1.38 (0.31), residues: 746 helix: 1.51 (0.21), residues: 568 sheet: 0.02 (0.75), residues: 42 loop : -1.24 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.002 0.001 HIS A 57 PHE 0.009 0.001 PHE A 603 TYR 0.006 0.001 TYR B 609 ARG 0.003 0.000 ARG B 489 *********************** 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 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 624 MET cc_start: 0.7646 (tpp) cc_final: 0.6142 (tpt) REVERT: A 624 MET cc_start: 0.7690 (tpt) cc_final: 0.6144 (tpt) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 2.1665 time to fit residues: 202.0276 Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 162 MET 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 59 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6066 Z= 0.344 Angle : 0.693 8.549 8266 Z= 0.367 Chirality : 0.044 0.189 990 Planarity : 0.007 0.057 998 Dihedral : 6.519 44.101 816 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.13 % Allowed : 9.09 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 746 helix: 1.01 (0.21), residues: 564 sheet: 0.06 (0.70), residues: 42 loop : -1.79 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 506 HIS 0.006 0.001 HIS A 187 PHE 0.011 0.002 PHE B 566 TYR 0.011 0.002 TYR B 498 ARG 0.006 0.001 ARG B 565 *********************** 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 112 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.899 Fit side-chains REVERT: B 133 MET cc_start: 0.8152 (mmp) cc_final: 0.7939 (mmm) REVERT: B 624 MET cc_start: 0.7928 (tpp) cc_final: 0.6710 (tpt) REVERT: A 624 MET cc_start: 0.7921 (tpt) cc_final: 0.6275 (tpt) outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 1.9262 time to fit residues: 214.6537 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER 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 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6066 Z= 0.210 Angle : 0.570 6.573 8266 Z= 0.300 Chirality : 0.039 0.134 990 Planarity : 0.006 0.054 998 Dihedral : 5.590 34.151 816 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.04 % Allowed : 11.76 % Favored : 86.21 % 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: 1.05 (0.30), residues: 746 helix: 1.32 (0.21), residues: 564 sheet: -0.05 (0.72), residues: 42 loop : -1.50 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 506 HIS 0.001 0.000 HIS A 57 PHE 0.010 0.001 PHE B 566 TYR 0.010 0.001 TYR A 635 ARG 0.003 0.000 ARG B 489 *********************** 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 95 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8211 (ttp) cc_final: 0.7778 (ttt) REVERT: B 133 MET cc_start: 0.8143 (mmp) cc_final: 0.7928 (mmm) REVERT: B 520 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7165 (mt) REVERT: B 624 MET cc_start: 0.7884 (tpp) cc_final: 0.6415 (tpt) REVERT: A 520 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7147 (mt) REVERT: A 624 MET cc_start: 0.7903 (tpt) cc_final: 0.6245 (tpt) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 2.2711 time to fit residues: 216.3493 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 162 MET 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 520 ILE Chi-restraints excluded: chain A residue 539 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 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6066 Z= 0.248 Angle : 0.585 5.899 8266 Z= 0.310 Chirality : 0.039 0.135 990 Planarity : 0.006 0.054 998 Dihedral : 5.625 34.659 816 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.35 % Allowed : 11.60 % Favored : 86.05 % 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: 1.09 (0.30), residues: 746 helix: 1.32 (0.21), residues: 568 sheet: -0.04 (0.71), residues: 42 loop : -1.44 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.003 0.001 HIS B 187 PHE 0.008 0.001 PHE A 45 TYR 0.009 0.001 TYR B 635 ARG 0.002 0.000 ARG B 489 *********************** 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 97 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8263 (ttp) cc_final: 0.7730 (ttt) REVERT: B 133 MET cc_start: 0.8165 (mmp) cc_final: 0.7953 (mmm) REVERT: B 624 MET cc_start: 0.7951 (tpp) cc_final: 0.6561 (tpt) REVERT: A 133 MET cc_start: 0.8213 (mmp) cc_final: 0.7998 (mmm) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 2.1606 time to fit residues: 208.1189 Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 29 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 539 SER 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 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.8644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6066 Z= 0.210 Angle : 0.552 5.519 8266 Z= 0.292 Chirality : 0.038 0.133 990 Planarity : 0.006 0.053 998 Dihedral : 5.290 30.248 816 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.04 % Allowed : 11.60 % Favored : 86.36 % 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: 1.22 (0.30), residues: 746 helix: 1.40 (0.21), residues: 568 sheet: -0.07 (0.72), residues: 42 loop : -1.26 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.002 0.001 HIS B 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 *********************** 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 100 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8286 (ttp) cc_final: 0.8046 (ttt) REVERT: B 70 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7476 (mmm-85) REVERT: B 133 MET cc_start: 0.8219 (mmp) cc_final: 0.8004 (mmm) REVERT: B 178 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: B 472 ASN cc_start: 0.6544 (OUTLIER) cc_final: 0.6153 (t0) REVERT: B 520 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7154 (mt) REVERT: B 624 MET cc_start: 0.7944 (tpp) cc_final: 0.6601 (tpt) REVERT: A 70 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7475 (mmm-85) REVERT: A 133 MET cc_start: 0.8217 (mmp) cc_final: 0.7998 (mmm) REVERT: A 178 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6070 (mp0) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 2.0470 time to fit residues: 208.3014 Evaluate side-chains 95 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 472 ASN 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 178 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 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 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.8802 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= 0.196 Angle : 0.547 5.188 8266 Z= 0.288 Chirality : 0.037 0.131 990 Planarity : 0.005 0.051 998 Dihedral : 4.928 24.333 816 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.41 % Allowed : 13.64 % 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: 1.44 (0.31), residues: 746 helix: 1.57 (0.21), residues: 568 sheet: -0.07 (0.74), residues: 42 loop : -1.22 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.002 0.001 HIS A 57 PHE 0.007 0.001 PHE A 45 TYR 0.009 0.001 TYR A 635 ARG 0.002 0.000 ARG A 493 *********************** 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 92 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8287 (ttp) cc_final: 0.7806 (ttt) REVERT: B 70 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7441 (mmm-85) REVERT: B 624 MET cc_start: 0.7933 (tpp) cc_final: 0.6556 (tpt) REVERT: A 70 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7429 (mmm-85) REVERT: A 133 MET cc_start: 0.8208 (mmp) cc_final: 0.7984 (mmm) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 2.0614 time to fit residues: 189.8386 Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 58 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6066 Z= 0.160 Angle : 0.529 10.293 8266 Z= 0.272 Chirality : 0.036 0.129 990 Planarity : 0.005 0.048 998 Dihedral : 4.407 17.191 816 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.10 % Allowed : 13.79 % Favored : 85.11 % 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: 1.76 (0.31), residues: 746 helix: 1.80 (0.21), residues: 568 sheet: -0.01 (0.75), residues: 42 loop : -1.11 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 144 HIS 0.002 0.001 HIS A 57 PHE 0.006 0.001 PHE A 45 TYR 0.007 0.001 TYR B 635 ARG 0.003 0.000 ARG A 565 ********************** 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 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8319 (ttp) cc_final: 0.8079 (ttt) REVERT: B 624 MET cc_start: 0.7864 (tpp) cc_final: 0.6633 (tpt) REVERT: A 133 MET cc_start: 0.8195 (mmp) cc_final: 0.7973 (mmm) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 2.1635 time to fit residues: 196.8171 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 54 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146518 restraints weight = 17508.019| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.16 r_work: 0.3561 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.8911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6066 Z= 0.167 Angle : 0.520 8.091 8266 Z= 0.270 Chirality : 0.036 0.131 990 Planarity : 0.005 0.048 998 Dihedral : 4.457 17.329 816 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.25 % Allowed : 13.79 % 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: 1.81 (0.31), residues: 746 helix: 1.84 (0.21), residues: 568 sheet: 0.00 (0.76), residues: 42 loop : -1.11 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.002 0.000 HIS A 57 PHE 0.008 0.001 PHE A 45 TYR 0.007 0.001 TYR A 635 ARG 0.002 0.000 ARG B 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.92 seconds wall clock time: 83 minutes 20.88 seconds (5000.88 seconds total)