Starting phenix.real_space_refine on Wed Mar 5 19:09:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vif_43260/03_2025/8vif_43260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vif_43260/03_2025/8vif_43260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vif_43260/03_2025/8vif_43260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vif_43260/03_2025/8vif_43260.map" model { file = "/net/cci-nas-00/data/ceres_data/8vif_43260/03_2025/8vif_43260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vif_43260/03_2025/8vif_43260.cif" } resolution = 3.1 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= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2109 2.51 5 N 557 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.53, per 1000 atoms: 1.36 Number of scatterers: 3326 At special positions: 0 Unit cell: (77.08, 81.78, 67.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 645 8.00 N 557 7.00 C 2109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.04 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R1301 " - " ASN R 343 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 414.3 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 11.9% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.547A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 100A No H-bonds generated for 'chain 'H' and resid 99 through 100A' Processing helix chain 'L' and resid 27A through 30 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.598A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 372 removed outlier: 3.524A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.651A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.023A pdb=" N VAL H 35A" --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA H 96 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE H 100K" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.449A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 124 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1060 1.34 - 1.46: 860 1.46 - 1.58: 1470 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3408 Sorted by residual: bond pdb=" C GLN H 39 " pdb=" N PRO H 40 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.15e-02 7.56e+03 6.15e+00 bond pdb=" N LYS H 43 " pdb=" CA LYS H 43 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.44e-02 4.82e+03 4.25e+00 bond pdb=" N GLY H 42 " pdb=" CA GLY H 42 " ideal model delta sigma weight residual 1.450 1.475 -0.025 1.38e-02 5.25e+03 3.22e+00 bond pdb=" C1 NAG R1301 " pdb=" O5 NAG R1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" CA LEU L 78 " pdb=" C LEU L 78 " ideal model delta sigma weight residual 1.529 1.517 0.012 1.04e-02 9.25e+03 1.31e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4311 1.07 - 2.14: 257 2.14 - 3.21: 49 3.21 - 4.28: 14 4.28 - 5.36: 4 Bond angle restraints: 4635 Sorted by residual: angle pdb=" N PRO H 40 " pdb=" CA PRO H 40 " pdb=" CB PRO H 40 " ideal model delta sigma weight residual 103.22 105.11 -1.89 5.20e-01 3.70e+00 1.32e+01 angle pdb=" C ASN L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 122.08 126.62 -4.54 1.47e+00 4.63e-01 9.52e+00 angle pdb=" CA GLY R 502 " pdb=" C GLY R 502 " pdb=" O GLY R 502 " ideal model delta sigma weight residual 122.29 120.15 2.14 8.10e-01 1.52e+00 6.96e+00 angle pdb=" CA LYS H 43 " pdb=" C LYS H 43 " pdb=" O LYS H 43 " ideal model delta sigma weight residual 121.49 118.46 3.03 1.16e+00 7.43e-01 6.80e+00 angle pdb=" CA GLY H 100C" pdb=" C GLY H 100C" pdb=" N TYR H 100D" ideal model delta sigma weight residual 114.85 117.19 -2.34 9.50e-01 1.11e+00 6.08e+00 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 1797 16.09 - 32.18: 173 32.18 - 48.26: 43 48.26 - 64.35: 12 64.35 - 80.44: 3 Dihedral angle restraints: 2028 sinusoidal: 794 harmonic: 1234 Sorted by residual: dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual 93.00 162.90 -69.90 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -45.89 -40.11 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA ASN H 97 " pdb=" C ASN H 97 " pdb=" N TYR H 98 " pdb=" CA TYR H 98 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 307 0.033 - 0.066: 139 0.066 - 0.100: 37 0.100 - 0.133: 25 0.133 - 0.166: 3 Chirality restraints: 511 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ASP H 99 " pdb=" N ASP H 99 " pdb=" C ASP H 99 " pdb=" CB ASP H 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 508 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 14 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO L 15 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO L 8 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 369 " 0.007 2.00e-02 2.50e+03 8.07e-03 1.30e+00 pdb=" CG TYR R 369 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR R 369 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR R 369 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 369 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 369 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 369 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 369 " 0.000 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 191 2.73 - 3.27: 3152 3.27 - 3.81: 5374 3.81 - 4.36: 6810 4.36 - 4.90: 11893 Nonbonded interactions: 27420 Sorted by model distance: nonbonded pdb=" O ASN H 31 " pdb=" OG SER H 53 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP H 55 " pdb=" NH1 ARG H 71 " model vdw 2.205 3.120 nonbonded pdb=" O ARG H 100F" pdb=" NH2 ARG L 96 " model vdw 2.364 3.120 nonbonded pdb=" NH2 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 2.368 3.120 nonbonded pdb=" OD1 ASN L 27B" pdb=" N ILE L 27C" model vdw 2.381 3.120 ... (remaining 27415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.037 3408 Z= 0.249 Angle : 0.613 5.356 4635 Z= 0.360 Chirality : 0.045 0.166 511 Planarity : 0.006 0.095 596 Dihedral : 13.827 80.441 1224 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 14.40 % Favored : 85.60 % 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: 0.05 (0.40), residues: 419 helix: -2.67 (1.00), residues: 19 sheet: 0.80 (0.45), residues: 146 loop : -0.16 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.010 0.001 PHE L 91 TYR 0.020 0.002 TYR R 369 ARG 0.002 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.443 Fit side-chains REVERT: H 41 PRO cc_start: 0.8750 (Cg_endo) cc_final: 0.8532 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1888 time to fit residues: 11.4406 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130958 restraints weight = 3475.106| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.68 r_work: 0.3124 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3408 Z= 0.217 Angle : 0.538 5.190 4635 Z= 0.288 Chirality : 0.045 0.151 511 Planarity : 0.005 0.065 596 Dihedral : 5.493 53.446 489 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.63 % Allowed : 14.67 % Favored : 83.70 % 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: 0.06 (0.40), residues: 419 helix: -2.97 (0.91), residues: 19 sheet: 0.57 (0.44), residues: 154 loop : 0.03 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.009 0.001 PHE L 62 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.387 Fit side-chains REVERT: H 43 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8267 (mttm) REVERT: H 56 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8018 (mm-30) REVERT: R 501 TYR cc_start: 0.7418 (m-10) cc_final: 0.7060 (m-10) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.1812 time to fit residues: 11.9226 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 17 optimal weight: 0.0070 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.2690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115876 restraints weight = 3523.806| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.29 r_work: 0.3142 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3408 Z= 0.164 Angle : 0.494 4.795 4635 Z= 0.262 Chirality : 0.043 0.146 511 Planarity : 0.005 0.053 596 Dihedral : 5.300 52.837 489 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.90 % Allowed : 16.30 % Favored : 81.79 % 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: -0.11 (0.40), residues: 419 helix: -3.56 (0.72), residues: 25 sheet: 0.57 (0.44), residues: 147 loop : -0.00 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.001 0.000 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.002 0.000 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.382 Fit side-chains REVERT: H 43 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8350 (mttm) REVERT: H 56 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8083 (mm-30) REVERT: R 501 TYR cc_start: 0.7452 (m-10) cc_final: 0.7181 (m-10) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.1380 time to fit residues: 9.5133 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN L 34 HIS R 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127940 restraints weight = 3537.737| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.15 r_work: 0.2944 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3408 Z= 0.258 Angle : 0.546 6.469 4635 Z= 0.287 Chirality : 0.045 0.154 511 Planarity : 0.005 0.047 596 Dihedral : 5.568 52.929 489 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.99 % Allowed : 16.58 % Favored : 80.43 % 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: -0.22 (0.39), residues: 419 helix: -3.84 (0.69), residues: 25 sheet: 0.56 (0.44), residues: 144 loop : -0.09 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.009 0.001 PHE L 91 TYR 0.024 0.002 TYR L 49 ARG 0.008 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.358 Fit side-chains REVERT: H 43 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8427 (mttm) REVERT: H 108 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8740 (tt) REVERT: R 501 TYR cc_start: 0.7462 (m-10) cc_final: 0.7193 (m-10) outliers start: 11 outliers final: 8 residues processed: 55 average time/residue: 0.1579 time to fit residues: 10.8885 Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.165259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126538 restraints weight = 3552.603| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.27 r_work: 0.3101 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3408 Z= 0.253 Angle : 0.531 6.767 4635 Z= 0.280 Chirality : 0.045 0.152 511 Planarity : 0.005 0.043 596 Dihedral : 5.566 52.873 489 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.99 % Allowed : 17.12 % Favored : 79.89 % 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: -0.28 (0.39), residues: 419 helix: -3.82 (0.70), residues: 25 sheet: 0.49 (0.45), residues: 142 loop : -0.12 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS L 34 PHE 0.008 0.001 PHE L 91 TYR 0.020 0.002 TYR L 49 ARG 0.004 0.000 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.371 Fit side-chains REVERT: H 43 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8402 (mttm) REVERT: L 79 GLN cc_start: 0.7519 (mp10) cc_final: 0.6914 (mt0) REVERT: R 501 TYR cc_start: 0.7548 (m-10) cc_final: 0.7343 (m-10) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.1458 time to fit residues: 9.8444 Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 37 optimal weight: 0.0000 chunk 33 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117718 restraints weight = 3643.735| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.32 r_work: 0.2983 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3408 Z= 0.178 Angle : 0.487 5.875 4635 Z= 0.257 Chirality : 0.043 0.148 511 Planarity : 0.004 0.041 596 Dihedral : 5.348 52.974 489 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.17 % Allowed : 17.93 % Favored : 79.89 % 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: -0.25 (0.40), residues: 419 helix: -3.81 (0.70), residues: 25 sheet: 0.50 (0.45), residues: 142 loop : -0.09 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS L 34 PHE 0.007 0.001 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.353 Fit side-chains REVERT: H 43 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8376 (mttm) REVERT: H 56 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8333 (mm-30) REVERT: L 32 ASP cc_start: 0.8536 (m-30) cc_final: 0.8324 (m-30) REVERT: L 79 GLN cc_start: 0.7577 (mp10) cc_final: 0.6873 (mt0) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.1248 time to fit residues: 9.0831 Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.154821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108349 restraints weight = 3625.902| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.32 r_work: 0.2799 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3408 Z= 0.319 Angle : 0.557 7.184 4635 Z= 0.294 Chirality : 0.046 0.153 511 Planarity : 0.005 0.039 596 Dihedral : 5.685 52.777 489 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.26 % Allowed : 17.39 % Favored : 79.35 % 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: -0.34 (0.40), residues: 419 helix: -3.87 (0.69), residues: 25 sheet: 0.45 (0.45), residues: 142 loop : -0.15 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS L 34 PHE 0.009 0.001 PHE L 91 TYR 0.024 0.002 TYR L 49 ARG 0.003 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.373 Fit side-chains REVERT: H 18 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7729 (tp) REVERT: H 43 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8364 (mttm) REVERT: L 79 GLN cc_start: 0.7635 (mp10) cc_final: 0.6915 (mt0) REVERT: R 501 TYR cc_start: 0.7462 (m-10) cc_final: 0.7098 (m-10) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1284 time to fit residues: 8.6891 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108864 restraints weight = 3630.023| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.32 r_work: 0.2870 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3408 Z= 0.270 Angle : 0.531 6.455 4635 Z= 0.281 Chirality : 0.045 0.152 511 Planarity : 0.005 0.038 596 Dihedral : 5.644 52.938 489 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 18.48 % Favored : 79.08 % 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: -0.40 (0.40), residues: 419 helix: -3.84 (0.71), residues: 25 sheet: 0.39 (0.44), residues: 144 loop : -0.20 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS L 34 PHE 0.009 0.001 PHE L 91 TYR 0.021 0.002 TYR L 49 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.378 Fit side-chains REVERT: L 79 GLN cc_start: 0.7649 (mp10) cc_final: 0.7014 (mt0) REVERT: R 414 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8762 (mm-40) REVERT: R 501 TYR cc_start: 0.7457 (m-10) cc_final: 0.7136 (m-10) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1346 time to fit residues: 8.6154 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104278 restraints weight = 3656.069| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.35 r_work: 0.3059 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3408 Z= 0.284 Angle : 0.545 6.775 4635 Z= 0.287 Chirality : 0.045 0.152 511 Planarity : 0.005 0.038 596 Dihedral : 5.682 52.920 489 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.45 % Allowed : 18.48 % Favored : 79.08 % 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: -0.46 (0.40), residues: 419 helix: -3.82 (0.71), residues: 25 sheet: 0.35 (0.45), residues: 142 loop : -0.24 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS L 34 PHE 0.009 0.001 PHE L 91 TYR 0.021 0.002 TYR L 49 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.381 Fit side-chains REVERT: L 79 GLN cc_start: 0.7676 (mp10) cc_final: 0.7084 (mt0) REVERT: R 414 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8786 (mm-40) REVERT: R 501 TYR cc_start: 0.7579 (m-10) cc_final: 0.7304 (m-10) outliers start: 9 outliers final: 9 residues processed: 51 average time/residue: 0.1351 time to fit residues: 8.9324 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105770 restraints weight = 3612.754| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.34 r_work: 0.2972 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3408 Z= 0.239 Angle : 0.523 6.442 4635 Z= 0.276 Chirality : 0.045 0.151 511 Planarity : 0.005 0.037 596 Dihedral : 5.581 52.980 489 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 18.48 % Favored : 79.35 % 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: -0.42 (0.40), residues: 419 helix: -3.80 (0.72), residues: 25 sheet: 0.35 (0.45), residues: 142 loop : -0.20 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS L 34 PHE 0.008 0.001 PHE L 91 TYR 0.019 0.001 TYR L 49 ARG 0.002 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.396 Fit side-chains REVERT: H 18 LEU cc_start: 0.7984 (tp) cc_final: 0.7734 (tp) REVERT: L 79 GLN cc_start: 0.7686 (mp10) cc_final: 0.7113 (mt0) REVERT: R 386 LYS cc_start: 0.7641 (pttt) cc_final: 0.7253 (ptpp) outliers start: 8 outliers final: 8 residues processed: 50 average time/residue: 0.1326 time to fit residues: 8.7223 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.0050 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110973 restraints weight = 3635.942| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.30 r_work: 0.3147 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3408 Z= 0.178 Angle : 0.490 5.922 4635 Z= 0.260 Chirality : 0.043 0.147 511 Planarity : 0.004 0.037 596 Dihedral : 5.387 53.018 489 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.63 % Allowed : 19.29 % Favored : 79.08 % 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: -0.29 (0.40), residues: 419 helix: -3.85 (0.70), residues: 27 sheet: 0.42 (0.45), residues: 144 loop : -0.05 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.002 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.67 seconds wall clock time: 42 minutes 25.12 seconds (2545.12 seconds total)