Starting phenix.real_space_refine on Mon Jan 13 17:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vif_43260/01_2025/8vif_43260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vif_43260/01_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_43260/01_2025/8vif_43260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vif_43260/01_2025/8vif_43260.map" model { file = "/net/cci-nas-00/data/ceres_data/8vif_43260/01_2025/8vif_43260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vif_43260/01_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-5571/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: 4.09, per 1000 atoms: 1.23 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: 0.77 Conformation dependent library (CDL) restraints added in 402.5 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: 0.94 Time building geometry restraints manager: 0.91 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: 3.400 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- 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 : 0.370 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: 0.1745 time to fit residues: 10.4981 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 : 0.385 ------------------------------------------------------------------------------- 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 = 0.130935 restraints weight = 3475.151| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.68 r_work: 0.3123 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 53.448 489 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 : 0.396 Fit side-chains REVERT: H 43 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8264 (mttm) REVERT: H 56 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8013 (mm-30) REVERT: R 501 TYR cc_start: 0.7416 (m-10) cc_final: 0.7057 (m-10) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.2175 time to fit residues: 14.6999 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 : 0.404 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110124 restraints weight = 3530.241| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.26 r_work: 0.3105 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3408 Z= 0.234 Angle : 0.534 5.448 4635 Z= 0.284 Chirality : 0.045 0.152 511 Planarity : 0.005 0.052 596 Dihedral : 5.527 52.784 489 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.45 % Allowed : 16.03 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.40), residues: 419 helix: -3.03 (0.91), residues: 19 sheet: 0.40 (0.43), residues: 154 loop : -0.08 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.009 0.001 PHE L 91 TYR 0.020 0.002 TYR L 49 ARG 0.003 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 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.373 Fit side-chains REVERT: H 43 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8373 (mttm) REVERT: R 501 TYR cc_start: 0.7547 (m-10) cc_final: 0.7241 (m-10) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.1332 time to fit residues: 9.0363 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 100 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.166357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128963 restraints weight = 3536.079| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.46 r_work: 0.3137 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1335 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= 0.233 Angle : 0.531 5.843 4635 Z= 0.280 Chirality : 0.045 0.152 511 Planarity : 0.005 0.047 596 Dihedral : 5.522 52.923 489 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.45 % Allowed : 16.03 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.40), residues: 419 helix: -3.61 (0.75), residues: 25 sheet: 0.42 (0.44), residues: 147 loop : -0.12 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.019 0.001 TYR L 49 ARG 0.003 0.000 ARG L 18 *********************** 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 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.291 Fit side-chains REVERT: H 43 LYS cc_start: 0.8714 (mmtp) cc_final: 0.8325 (mttm) REVERT: H 108 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8729 (tt) REVERT: R 501 TYR cc_start: 0.7488 (m-10) cc_final: 0.7257 (m-10) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1480 time to fit residues: 9.9972 Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 108 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.155782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109751 restraints weight = 3603.316| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.28 r_work: 0.2935 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.198 Angle : 0.506 5.471 4635 Z= 0.268 Chirality : 0.044 0.150 511 Planarity : 0.005 0.042 596 Dihedral : 5.429 52.898 489 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.45 % Allowed : 16.58 % Favored : 80.98 % 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: -0.30 (0.40), residues: 419 helix: -3.58 (0.75), residues: 25 sheet: 0.41 (0.44), residues: 147 loop : -0.12 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.017 0.001 TYR L 49 ARG 0.004 0.000 ARG L 18 *********************** 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 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.316 Fit side-chains REVERT: H 43 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8371 (mttm) REVERT: H 56 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8313 (mm-30) REVERT: L 79 GLN cc_start: 0.7462 (mp10) cc_final: 0.6757 (mt0) REVERT: R 501 TYR cc_start: 0.7495 (m-10) cc_final: 0.7257 (m-10) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.1494 time to fit residues: 10.6260 Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.153986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107363 restraints weight = 3678.423| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.34 r_work: 0.2981 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3408 Z= 0.256 Angle : 0.534 6.402 4635 Z= 0.281 Chirality : 0.045 0.152 511 Planarity : 0.005 0.040 596 Dihedral : 5.567 52.849 489 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 16.58 % Favored : 80.71 % 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: -0.35 (0.39), residues: 419 helix: -3.74 (0.72), residues: 25 sheet: 0.44 (0.45), residues: 142 loop : -0.18 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.021 0.002 TYR L 49 ARG 0.007 0.001 ARG R 403 *********************** 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 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.385 Fit side-chains REVERT: H 18 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7919 (tp) REVERT: L 79 GLN cc_start: 0.7570 (mp10) cc_final: 0.6937 (mt0) REVERT: R 501 TYR cc_start: 0.7495 (m-10) cc_final: 0.7277 (m-10) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.1578 time to fit residues: 10.4635 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 : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 441 LEU 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: 0.9980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 4 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 R 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106707 restraints weight = 3622.213| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.30 r_work: 0.2937 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1887 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= 0.279 Angle : 0.541 6.775 4635 Z= 0.286 Chirality : 0.045 0.153 511 Planarity : 0.005 0.038 596 Dihedral : 5.666 52.897 489 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 16.85 % Favored : 80.16 % 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: -0.44 (0.39), residues: 419 helix: -3.80 (0.70), residues: 25 sheet: 0.41 (0.47), residues: 133 loop : -0.24 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.009 0.001 PHE L 91 TYR 0.021 0.002 TYR L 49 ARG 0.005 0.000 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 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.371 Fit side-chains REVERT: L 79 GLN cc_start: 0.7712 (mp10) cc_final: 0.7032 (mt0) REVERT: R 501 TYR cc_start: 0.7614 (m-10) cc_final: 0.7360 (m-10) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.1342 time to fit residues: 8.8351 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 100 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0670 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106844 restraints weight = 3633.917| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.36 r_work: 0.2922 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.200 Angle : 0.519 6.111 4635 Z= 0.271 Chirality : 0.044 0.150 511 Planarity : 0.005 0.037 596 Dihedral : 5.541 52.954 489 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.63 % Allowed : 18.75 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.39), residues: 419 helix: -3.69 (0.74), residues: 25 sheet: 0.40 (0.45), residues: 144 loop : -0.21 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS L 34 PHE 0.007 0.001 PHE L 91 TYR 0.018 0.001 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 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.384 Fit side-chains REVERT: H 43 LYS cc_start: 0.8656 (mttm) cc_final: 0.8443 (mttm) REVERT: L 79 GLN cc_start: 0.7720 (mp10) cc_final: 0.7075 (mt0) REVERT: R 501 TYR cc_start: 0.7582 (m-10) cc_final: 0.7364 (m-10) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1325 time to fit residues: 8.4190 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 415 THR 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: 0.0270 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107544 restraints weight = 3640.030| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.36 r_work: 0.3129 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.197 Angle : 0.511 6.017 4635 Z= 0.267 Chirality : 0.044 0.150 511 Planarity : 0.004 0.037 596 Dihedral : 5.462 52.963 489 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.63 % Allowed : 19.02 % 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: -0.39 (0.40), residues: 419 helix: -3.67 (0.75), residues: 25 sheet: 0.41 (0.45), residues: 144 loop : -0.21 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.015 0.001 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 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.518 Fit side-chains REVERT: H 18 LEU cc_start: 0.7722 (tp) cc_final: 0.7464 (tt) REVERT: L 79 GLN cc_start: 0.7650 (mp10) cc_final: 0.7145 (mt0) REVERT: R 386 LYS cc_start: 0.7682 (pttt) cc_final: 0.7299 (ptpp) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.1415 time to fit residues: 8.7668 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.0170 chunk 38 optimal weight: 0.0030 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 overall best weight: 0.1706 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.156436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110806 restraints weight = 3607.812| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.34 r_work: 0.3076 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3408 Z= 0.142 Angle : 0.474 5.480 4635 Z= 0.250 Chirality : 0.043 0.145 511 Planarity : 0.004 0.037 596 Dihedral : 5.229 53.079 489 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.09 % Allowed : 19.84 % 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: -0.25 (0.40), residues: 419 helix: -3.58 (0.77), residues: 25 sheet: 0.56 (0.45), residues: 144 loop : -0.17 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.005 0.001 PHE L 91 TYR 0.009 0.001 TYR L 49 ARG 0.003 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 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.376 Fit side-chains REVERT: H 56 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8419 (mm-30) REVERT: L 79 GLN cc_start: 0.7560 (mp10) cc_final: 0.7049 (mt0) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1298 time to fit residues: 8.1638 Evaluate side-chains 47 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN L 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105120 restraints weight = 3631.299| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.37 r_work: 0.3105 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3408 Z= 0.287 Angle : 0.541 6.959 4635 Z= 0.287 Chirality : 0.045 0.150 511 Planarity : 0.005 0.037 596 Dihedral : 5.583 52.813 489 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.36 % Allowed : 20.65 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.40), residues: 419 helix: -3.72 (0.73), residues: 25 sheet: 0.46 (0.46), residues: 142 loop : -0.25 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 34 PHE 0.009 0.001 PHE L 62 TYR 0.021 0.002 TYR L 49 ARG 0.003 0.001 ARG R 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.06 seconds wall clock time: 42 minutes 31.83 seconds (2551.83 seconds total)