Starting phenix.real_space_refine on Mon Dec 30 02:37:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xxb_33500/12_2024/7xxb_33500_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xxb_33500/12_2024/7xxb_33500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xxb_33500/12_2024/7xxb_33500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xxb_33500/12_2024/7xxb_33500.map" model { file = "/net/cci-nas-00/data/ceres_data/7xxb_33500/12_2024/7xxb_33500_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xxb_33500/12_2024/7xxb_33500_trim.cif" } resolution = 2.93 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= 0.003 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 3922 2.51 5 N 940 2.21 5 O 996 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-5532/modules/chem_data/mon_lib" Total number of atoms: 12038 Number of models: 1 Model: "" Number of chains: 4 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: 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.49 Number of scatterers: 12038 At special positions: 0 Unit cell: (80.91, 121.83, 69.75, 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 996 8.00 N 940 7.00 C 3922 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: 3.48 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: 36 helices and 2 sheets defined 79.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.943A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.650A pdb=" N ASN A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 68 through 91 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 143 Processing helix chain 'A' and resid 143 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 475 through 492 Processing helix chain 'A' and resid 494 through 513 Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.402A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 554 through 581 removed outlier: 3.883A 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 584 through 595 Processing helix chain 'A' and resid 599 through 609 removed outlier: 4.035A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 626 through 640 removed outlier: 3.706A pdb=" N ILE A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 62 removed outlier: 4.944A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.650A pdb=" N ASN B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 92 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 126 through 143 Processing helix chain 'B' and resid 143 through 165 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 475 through 492 Processing helix chain 'B' and resid 494 through 513 Processing helix chain 'B' and resid 518 through 530 removed outlier: 4.390A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 Processing helix chain 'B' and resid 554 through 581 removed outlier: 3.885A 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 584 through 595 Processing helix chain 'B' and resid 599 through 609 removed outlier: 4.038A pdb=" N PHE B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.690A pdb=" N ILE B 630 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 7.571A pdb=" N VAL A 204 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 175 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 206 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 177 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LYS A 208 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177 removed outlier: 7.593A pdb=" N VAL B 204 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B 175 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL B 206 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 177 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LYS B 208 " --> pdb=" O VAL B 177 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1326 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: 4.66 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6132 1.03 - 1.23: 8 1.23 - 1.42: 2460 1.42 - 1.61: 3506 1.61 - 1.81: 78 Bond restraints: 12184 Sorted by residual: bond pdb=" ND2 ASN A 112 " pdb="HD21 ASN A 112 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 112 " pdb="HD21 ASN B 112 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+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=" 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 3.58e+01 bond pdb=" N IAC B 701 " pdb=" C IAC B 701 " ideal model delta sigma weight residual 1.363 1.433 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 12179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 22089 5.95 - 11.90: 13 11.90 - 17.85: 0 17.85 - 23.80: 12 23.80 - 29.75: 18 Bond angle restraints: 22132 Sorted by residual: angle pdb=" HZ1 LYS A 158 " pdb=" NZ LYS A 158 " pdb=" HZ3 LYS A 158 " ideal model delta sigma weight residual 109.00 79.25 29.75 3.00e+00 1.11e-01 9.83e+01 angle pdb=" CG LEU A 504 " pdb=" CD2 LEU A 504 " pdb="HD22 LEU A 504 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" HZ1 LYS B 158 " pdb=" NZ LYS B 158 " pdb=" HZ3 LYS B 158 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CG LEU B 504 " pdb=" CD2 LEU B 504 " pdb="HD22 LEU B 504 " ideal model delta sigma weight residual 109.00 79.35 29.65 3.00e+00 1.11e-01 9.77e+01 angle pdb=" HZ1 LYS A 158 " pdb=" NZ LYS A 158 " pdb=" HZ2 LYS A 158 " ideal model delta sigma weight residual 109.00 79.39 29.61 3.00e+00 1.11e-01 9.74e+01 ... (remaining 22127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 5011 14.09 - 28.17: 465 28.17 - 42.26: 137 42.26 - 56.35: 73 56.35 - 70.44: 12 Dihedral angle restraints: 5698 sinusoidal: 3054 harmonic: 2644 Sorted by residual: dihedral pdb=" CA LYS A 549 " pdb=" C LYS A 549 " pdb=" N LEU A 550 " pdb=" CA LEU A 550 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LYS B 549 " pdb=" C LYS B 549 " pdb=" N LEU B 550 " pdb=" CA LEU B 550 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LEU B 625 " pdb=" C LEU B 625 " pdb=" N ILE B 626 " pdb=" CA ILE B 626 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.350: 988 0.350 - 0.700: 0 0.700 - 1.050: 0 1.050 - 1.399: 0 1.399 - 1.749: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CG LEU B 550 " pdb=" CB LEU B 550 " pdb=" CD1 LEU B 550 " pdb=" CD2 LEU B 550 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.65e+01 chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CA ILE A 551 " pdb=" N ILE A 551 " pdb=" C ILE A 551 " pdb=" CB ILE A 551 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 987 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 140 " -0.156 2.00e-02 2.50e+03 1.75e-01 4.60e+02 pdb=" CD GLN A 140 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 140 " 0.150 2.00e-02 2.50e+03 pdb=" NE2 GLN A 140 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 140 " -0.265 2.00e-02 2.50e+03 pdb="HE22 GLN A 140 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 140 " -0.153 2.00e-02 2.50e+03 1.72e-01 4.42e+02 pdb=" CD GLN B 140 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 140 " 0.148 2.00e-02 2.50e+03 pdb=" NE2 GLN B 140 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 140 " 0.254 2.00e-02 2.50e+03 pdb="HE22 GLN B 140 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 112 " -0.137 2.00e-02 2.50e+03 1.36e-01 2.78e+02 pdb=" CG ASN A 112 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 112 " 0.131 2.00e-02 2.50e+03 pdb=" ND2 ASN A 112 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 112 " -0.196 2.00e-02 2.50e+03 pdb="HD22 ASN A 112 " 0.191 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 714 2.21 - 2.80: 25812 2.80 - 3.40: 35101 3.40 - 4.00: 45022 4.00 - 4.60: 70411 Nonbonded interactions: 177060 Sorted by model distance: nonbonded pdb=" H GLY B 197 " pdb=" O LYS B 201 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU A 163 " pdb="HE21 GLN A 164 " model vdw 1.610 2.450 nonbonded pdb=" OE1 GLU B 163 " pdb="HE21 GLN B 164 " model vdw 1.611 2.450 nonbonded pdb=" H GLY A 197 " pdb=" O LYS A 201 " model vdw 1.615 2.450 nonbonded pdb=" O SER A 27 " pdb=" H ILE A 33 " model vdw 1.636 2.450 ... (remaining 177055 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: 0.560 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: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.690 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.070 6046 Z= 0.245 Angle : 0.677 11.558 8238 Z= 0.343 Chirality : 0.086 1.749 990 Planarity : 0.005 0.053 994 Dihedral : 12.236 70.436 2122 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.68 (0.31), residues: 746 helix: 0.91 (0.22), residues: 548 sheet: 0.67 (0.75), residues: 42 loop : -1.01 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 506 HIS 0.004 0.001 HIS A 57 PHE 0.012 0.001 PHE A 603 TYR 0.024 0.002 TYR A 18 ARG 0.008 0.001 ARG B 583 *********************** 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 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 ILE cc_start: 0.8479 (mm) cc_final: 0.8269 (mp) REVERT: A 610 ASN cc_start: 0.8175 (t0) cc_final: 0.7956 (t0) REVERT: B 610 ASN cc_start: 0.8117 (t0) cc_final: 0.7903 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.6236 time to fit residues: 189.1751 Evaluate side-chains 95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 0.4980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7497 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6046 Z= 0.235 Angle : 0.594 11.016 8238 Z= 0.306 Chirality : 0.085 1.703 990 Planarity : 0.005 0.039 994 Dihedral : 4.618 33.599 804 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.25 % Allowed : 7.52 % Favored : 91.22 % 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: 0.84 (0.30), residues: 746 helix: 1.02 (0.22), residues: 552 sheet: 0.75 (0.76), residues: 42 loop : -0.98 (0.50), residues: 152 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 0.012 0.001 PHE A 45 TYR 0.018 0.001 TYR A 18 ARG 0.005 0.001 ARG A 583 *********************** 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 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 ILE cc_start: 0.8501 (mm) cc_final: 0.8294 (mp) REVERT: A 610 ASN cc_start: 0.8155 (t0) cc_final: 0.7910 (t0) REVERT: B 6 ASP cc_start: 0.7819 (m-30) cc_final: 0.7601 (m-30) REVERT: B 610 ASN cc_start: 0.8122 (t0) cc_final: 0.7862 (t0) outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 1.5821 time to fit residues: 193.1025 Evaluate side-chains 98 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6046 Z= 0.248 Angle : 0.585 10.657 8238 Z= 0.299 Chirality : 0.085 1.692 990 Planarity : 0.005 0.042 994 Dihedral : 4.583 33.270 804 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.10 % Allowed : 8.46 % Favored : 90.44 % 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: 0.89 (0.30), residues: 746 helix: 1.08 (0.22), residues: 552 sheet: 0.88 (0.77), residues: 42 loop : -1.10 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.004 0.001 HIS B 57 PHE 0.012 0.001 PHE A 45 TYR 0.018 0.001 TYR B 18 ARG 0.006 0.001 ARG B 565 *********************** 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 110 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 ILE cc_start: 0.8499 (mm) cc_final: 0.8290 (mp) REVERT: A 610 ASN cc_start: 0.8162 (t0) cc_final: 0.7855 (t0) REVERT: B 6 ASP cc_start: 0.7856 (m-30) cc_final: 0.7638 (m-30) REVERT: B 44 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7651 (ttt180) REVERT: B 610 ASN cc_start: 0.8194 (t0) cc_final: 0.7897 (t0) outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 1.6394 time to fit residues: 189.0127 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 499 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7547 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6046 Z= 0.300 Angle : 0.602 10.484 8238 Z= 0.309 Chirality : 0.085 1.696 990 Planarity : 0.005 0.041 994 Dihedral : 4.673 35.462 804 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.72 % Allowed : 9.56 % Favored : 88.71 % 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: 0.96 (0.30), residues: 746 helix: 1.13 (0.22), residues: 552 sheet: 1.05 (0.78), residues: 42 loop : -1.14 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 506 HIS 0.006 0.001 HIS A 57 PHE 0.013 0.001 PHE B 45 TYR 0.015 0.002 TYR A 18 ARG 0.006 0.001 ARG B 565 *********************** 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 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8253 (t0) cc_final: 0.7888 (t0) REVERT: B 6 ASP cc_start: 0.7875 (m-30) cc_final: 0.7651 (m-30) REVERT: B 608 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6486 (mt-10) REVERT: B 610 ASN cc_start: 0.8274 (t0) cc_final: 0.7926 (t0) outliers start: 11 outliers final: 2 residues processed: 110 average time/residue: 1.6256 time to fit residues: 192.8945 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6046 Z= 0.238 Angle : 0.580 10.452 8238 Z= 0.296 Chirality : 0.085 1.701 990 Planarity : 0.005 0.041 994 Dihedral : 4.629 35.525 804 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.25 % Allowed : 10.50 % Favored : 88.24 % 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: 1.21 (0.22), residues: 552 sheet: 1.15 (0.79), residues: 42 loop : -1.02 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.004 0.001 HIS B 57 PHE 0.012 0.001 PHE A 45 TYR 0.011 0.001 TYR B 635 ARG 0.005 0.000 ARG B 44 *********************** 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 113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6359 (mt-10) REVERT: A 610 ASN cc_start: 0.8266 (t0) cc_final: 0.7916 (t0) REVERT: B 6 ASP cc_start: 0.7867 (m-30) cc_final: 0.7652 (m-30) REVERT: B 608 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6381 (mt-10) REVERT: B 610 ASN cc_start: 0.8270 (t0) cc_final: 0.7903 (t0) outliers start: 8 outliers final: 2 residues processed: 109 average time/residue: 1.7200 time to fit residues: 201.1967 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6046 Z= 0.188 Angle : 0.569 10.448 8238 Z= 0.285 Chirality : 0.085 1.709 990 Planarity : 0.005 0.040 994 Dihedral : 4.511 34.188 804 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.25 % Allowed : 11.91 % Favored : 86.83 % 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: 1.29 (0.31), residues: 746 helix: 1.33 (0.22), residues: 552 sheet: 1.25 (0.78), residues: 42 loop : -0.89 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.004 0.001 HIS A 57 PHE 0.011 0.001 PHE B 92 TYR 0.011 0.001 TYR A 635 ARG 0.002 0.000 ARG B 565 *********************** 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 111 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: A 610 ASN cc_start: 0.8246 (t0) cc_final: 0.7867 (t0) REVERT: B 6 ASP cc_start: 0.7854 (m-30) cc_final: 0.7648 (m-30) REVERT: B 608 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6349 (mt-10) REVERT: B 610 ASN cc_start: 0.8238 (t0) cc_final: 0.7877 (t0) outliers start: 8 outliers final: 0 residues processed: 108 average time/residue: 1.4527 time to fit residues: 170.3198 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7538 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6046 Z= 0.230 Angle : 0.575 10.344 8238 Z= 0.290 Chirality : 0.085 1.702 990 Planarity : 0.005 0.039 994 Dihedral : 4.512 33.828 804 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.94 % Allowed : 12.85 % 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: 1.30 (0.30), residues: 746 helix: 1.35 (0.22), residues: 552 sheet: 0.97 (0.78), residues: 44 loop : -0.88 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.004 0.001 HIS B 57 PHE 0.016 0.001 PHE A 92 TYR 0.012 0.001 TYR B 635 ARG 0.004 0.000 ARG B 565 *********************** 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 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 610 ASN cc_start: 0.8281 (t0) cc_final: 0.7893 (t0) REVERT: B 44 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7562 (ttt180) REVERT: B 608 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: B 610 ASN cc_start: 0.8278 (t0) cc_final: 0.7903 (t0) outliers start: 6 outliers final: 2 residues processed: 113 average time/residue: 1.5105 time to fit residues: 185.2864 Evaluate side-chains 104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7543 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6046 Z= 0.234 Angle : 0.583 10.299 8238 Z= 0.294 Chirality : 0.085 1.708 990 Planarity : 0.005 0.039 994 Dihedral : 4.511 34.026 804 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.94 % Allowed : 13.79 % Favored : 85.27 % 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: 1.27 (0.30), residues: 746 helix: 1.34 (0.21), residues: 552 sheet: 1.01 (0.78), residues: 44 loop : -0.93 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.004 0.001 HIS A 57 PHE 0.015 0.001 PHE B 92 TYR 0.015 0.001 TYR A 635 ARG 0.002 0.000 ARG B 565 *********************** 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 112 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.4825 (OUTLIER) cc_final: 0.4495 (ptm) REVERT: A 608 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 610 ASN cc_start: 0.8282 (t0) cc_final: 0.7919 (t0) REVERT: B 44 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7531 (ttt180) REVERT: B 608 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6337 (mt-10) REVERT: B 610 ASN cc_start: 0.8280 (t0) cc_final: 0.7904 (t0) outliers start: 6 outliers final: 3 residues processed: 109 average time/residue: 1.5942 time to fit residues: 187.5214 Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6046 Z= 0.227 Angle : 0.587 10.159 8238 Z= 0.297 Chirality : 0.085 1.706 990 Planarity : 0.005 0.040 994 Dihedral : 4.510 34.120 804 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.57 % Allowed : 13.17 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.30), residues: 746 helix: 1.33 (0.21), residues: 552 sheet: 1.38 (0.77), residues: 42 loop : -1.06 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.004 0.001 HIS B 57 PHE 0.012 0.001 PHE A 92 TYR 0.015 0.001 TYR B 635 ARG 0.002 0.000 ARG A 44 *********************** 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 115 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4494 (ptm) REVERT: A 608 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: A 610 ASN cc_start: 0.8284 (t0) cc_final: 0.7920 (t0) REVERT: B 44 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7597 (ttt180) REVERT: B 608 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: B 610 ASN cc_start: 0.8296 (t0) cc_final: 0.7909 (t0) outliers start: 10 outliers final: 4 residues processed: 111 average time/residue: 1.5206 time to fit residues: 183.2248 Evaluate side-chains 109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 91 ASN B 547 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6046 Z= 0.182 Angle : 0.580 10.059 8238 Z= 0.290 Chirality : 0.085 1.712 990 Planarity : 0.005 0.040 994 Dihedral : 4.408 32.871 804 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.10 % Allowed : 13.48 % Favored : 85.42 % 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: 1.38 (0.21), residues: 552 sheet: 1.39 (0.77), residues: 42 loop : -1.06 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.003 0.001 HIS A 57 PHE 0.023 0.001 PHE A 92 TYR 0.012 0.001 TYR B 635 ARG 0.001 0.000 ARG B 70 ********************** 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 109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.4884 (OUTLIER) cc_final: 0.4561 (ptm) REVERT: A 608 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: A 610 ASN cc_start: 0.8262 (t0) cc_final: 0.7893 (t0) REVERT: B 44 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7522 (ttt180) REVERT: B 65 TYR cc_start: 0.8958 (m-80) cc_final: 0.8724 (m-80) REVERT: B 473 MET cc_start: 0.4875 (OUTLIER) cc_final: 0.4511 (ptm) REVERT: B 608 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: B 610 ASN cc_start: 0.8273 (t0) cc_final: 0.7910 (t0) outliers start: 7 outliers final: 2 residues processed: 104 average time/residue: 1.6182 time to fit residues: 181.2143 Evaluate side-chains 105 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 547 GLN B 547 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136023 restraints weight = 21342.340| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.61 r_work: 0.3505 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6046 Z= 0.171 Angle : 0.574 9.948 8238 Z= 0.285 Chirality : 0.085 1.703 990 Planarity : 0.005 0.041 994 Dihedral : 4.345 31.550 804 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.10 % Allowed : 13.95 % 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: 1.39 (0.30), residues: 746 helix: 1.43 (0.21), residues: 552 sheet: 1.52 (0.78), residues: 42 loop : -1.04 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.002 0.000 HIS B 57 PHE 0.009 0.001 PHE B 45 TYR 0.012 0.001 TYR B 635 ARG 0.001 0.000 ARG B 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4382.13 seconds wall clock time: 78 minutes 12.06 seconds (4692.06 seconds total)