Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 19:52:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/10_2023/7wlc_32581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/10_2023/7wlc_32581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/10_2023/7wlc_32581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/10_2023/7wlc_32581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/10_2023/7wlc_32581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/10_2023/7wlc_32581.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.009 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 14 5.16 5 C 2094 2.51 5 N 563 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3307 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.90, per 1000 atoms: 0.88 Number of scatterers: 3307 At special positions: 0 Unit cell: (53.04, 80.08, 95.68, 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 14 16.00 O 636 8.00 N 563 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 620.4 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 removed outlier: 3.657A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.535A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.569A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.730A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.730A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.634A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.789A pdb=" N GLU H 10 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 100 hydrogen bonds defined for protein. 237 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: 0.97 Time building geometry restraints manager: 1.90 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: 1071 1.34 - 1.47: 889 1.47 - 1.59: 1416 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3392 Sorted by residual: bond pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ASN E 448 " pdb=" CG ASN E 448 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 1.444 1.454 -0.010 9.60e-03 1.09e+04 9.95e-01 bond pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.85e-01 bond pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.82e-01 ... (remaining 3387 not shown) Histogram of bond angle deviations from ideal: 102.09 - 108.48: 187 108.48 - 114.87: 1827 114.87 - 121.26: 1591 121.26 - 127.65: 979 127.65 - 134.04: 30 Bond angle restraints: 4614 Sorted by residual: angle pdb=" C ASN E 331 " pdb=" N ILE E 332 " pdb=" CA ILE E 332 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA MET H 81 " pdb=" CB MET H 81 " pdb=" CG MET H 81 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 111.30 119.20 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 103.11 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA TRP H 111 " pdb=" CB TRP H 111 " pdb=" CG TRP H 111 " ideal model delta sigma weight residual 113.60 119.66 -6.06 1.90e+00 2.77e-01 1.02e+01 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1779 15.37 - 30.74: 175 30.74 - 46.11: 29 46.11 - 61.48: 13 61.48 - 76.85: 8 Dihedral angle restraints: 2004 sinusoidal: 768 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.64 64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.26 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA MET H 81 " pdb=" C MET H 81 " pdb=" N GLU H 82 " pdb=" CA GLU H 82 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 244 0.028 - 0.056: 160 0.056 - 0.084: 57 0.084 - 0.111: 25 0.111 - 0.139: 11 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO E 373 " pdb=" N PRO E 373 " pdb=" C PRO E 373 " pdb=" CB PRO E 373 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 494 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO L 60 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " -0.015 2.00e-02 2.50e+03 9.52e-03 2.27e+00 pdb=" CG TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO E 337 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " 0.019 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 234 2.74 - 3.28: 3348 3.28 - 3.82: 5244 3.82 - 4.36: 5995 4.36 - 4.90: 10460 Nonbonded interactions: 25281 Sorted by model distance: nonbonded pdb=" O ASN E 448 " pdb=" OG SER E 494 " model vdw 2.198 2.440 nonbonded pdb=" NZ LYS H 23 " pdb=" O THR H 76 " model vdw 2.242 2.520 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 115 " model vdw 2.263 2.440 nonbonded pdb=" O TYR H 108 " pdb=" OH TYR L 37 " model vdw 2.264 2.440 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.271 2.440 ... (remaining 25276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.003 0.034 3392 Z= 0.193 Angle : 0.701 9.586 4614 Z= 0.378 Chirality : 0.044 0.139 497 Planarity : 0.005 0.039 601 Dihedral : 13.708 76.851 1202 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.42), residues: 424 helix: -3.38 (0.98), residues: 18 sheet: 0.25 (0.50), residues: 131 loop : -1.37 (0.38), residues: 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1802 time to fit residues: 20.8917 Evaluate side-chains 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 50.0000 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 20 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3392 Z= 0.176 Angle : 0.686 10.252 4614 Z= 0.348 Chirality : 0.046 0.137 497 Planarity : 0.005 0.039 601 Dihedral : 5.306 19.543 471 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.39 % Allowed : 16.16 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.41), residues: 424 helix: -3.55 (1.21), residues: 12 sheet: 0.23 (0.49), residues: 133 loop : -1.34 (0.36), residues: 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 82 average time/residue: 0.1780 time to fit residues: 17.4487 Evaluate side-chains 76 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0401 time to fit residues: 0.7793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 50.0000 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 37 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 50.0000 chunk 28 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3392 Z= 0.158 Angle : 0.656 9.728 4614 Z= 0.329 Chirality : 0.045 0.135 497 Planarity : 0.004 0.039 601 Dihedral : 5.212 19.332 471 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.39 % Allowed : 16.43 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.41), residues: 424 helix: -4.31 (0.59), residues: 25 sheet: 0.40 (0.49), residues: 131 loop : -1.21 (0.37), residues: 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 87 average time/residue: 0.1936 time to fit residues: 19.7222 Evaluate side-chains 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0360 time to fit residues: 0.7205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 50.0000 chunk 40 optimal weight: 50.0000 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 40.0000 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 overall best weight: 7.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3392 Z= 0.239 Angle : 0.682 10.384 4614 Z= 0.347 Chirality : 0.045 0.136 497 Planarity : 0.004 0.042 601 Dihedral : 5.411 19.623 471 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.51 % Allowed : 19.50 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.41), residues: 424 helix: -4.01 (0.92), residues: 18 sheet: 0.40 (0.46), residues: 144 loop : -1.51 (0.37), residues: 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1944 time to fit residues: 18.7380 Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0470 time to fit residues: 1.1016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 40.0000 chunk 16 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3392 Z= 0.348 Angle : 0.753 11.242 4614 Z= 0.391 Chirality : 0.047 0.152 497 Planarity : 0.005 0.044 601 Dihedral : 5.868 20.371 471 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.95 % Allowed : 22.28 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.40), residues: 424 helix: -3.64 (1.26), residues: 12 sheet: 0.19 (0.46), residues: 137 loop : -1.65 (0.36), residues: 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.2021 time to fit residues: 19.7822 Evaluate side-chains 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0362 time to fit residues: 0.7604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 33 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3392 Z= 0.208 Angle : 0.697 10.906 4614 Z= 0.352 Chirality : 0.046 0.139 497 Planarity : 0.004 0.045 601 Dihedral : 5.567 20.502 471 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.39 % Allowed : 23.96 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.40), residues: 424 helix: -3.55 (1.33), residues: 12 sheet: 0.05 (0.46), residues: 139 loop : -1.53 (0.36), residues: 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 81 average time/residue: 0.2043 time to fit residues: 19.3762 Evaluate side-chains 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0414 time to fit residues: 0.8774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 50.0000 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3392 Z= 0.198 Angle : 0.704 8.013 4614 Z= 0.355 Chirality : 0.046 0.146 497 Planarity : 0.004 0.045 601 Dihedral : 5.502 21.172 471 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.11 % Allowed : 25.63 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 424 helix: -3.48 (1.32), residues: 12 sheet: 0.02 (0.46), residues: 139 loop : -1.42 (0.37), residues: 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.2082 time to fit residues: 19.1676 Evaluate side-chains 70 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0350 time to fit residues: 0.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3392 Z= 0.268 Angle : 0.734 9.029 4614 Z= 0.374 Chirality : 0.047 0.178 497 Planarity : 0.004 0.046 601 Dihedral : 5.719 21.560 471 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.39 % Allowed : 26.46 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.41), residues: 424 helix: -3.35 (0.92), residues: 18 sheet: -0.04 (0.47), residues: 138 loop : -1.53 (0.37), residues: 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.2046 time to fit residues: 18.4950 Evaluate side-chains 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0520 time to fit residues: 0.8136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 33 optimal weight: 40.0000 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 overall best weight: 6.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3392 Z= 0.226 Angle : 0.725 7.914 4614 Z= 0.371 Chirality : 0.046 0.155 497 Planarity : 0.004 0.045 601 Dihedral : 5.652 21.996 471 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.84 % Allowed : 27.02 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.41), residues: 424 helix: -3.59 (0.99), residues: 18 sheet: -0.18 (0.49), residues: 130 loop : -1.38 (0.37), residues: 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.2084 time to fit residues: 18.8271 Evaluate side-chains 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0394 time to fit residues: 0.6752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 50.0000 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 40.0000 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3392 Z= 0.238 Angle : 0.744 8.065 4614 Z= 0.380 Chirality : 0.047 0.181 497 Planarity : 0.004 0.046 601 Dihedral : 5.716 21.929 471 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.84 % Allowed : 28.41 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.41), residues: 424 helix: -3.54 (0.73), residues: 24 sheet: -0.26 (0.48), residues: 130 loop : -1.36 (0.38), residues: 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 0.2020 time to fit residues: 17.3515 Evaluate side-chains 75 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0430 time to fit residues: 0.7124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 40.0000 chunk 15 optimal weight: 0.0170 chunk 41 optimal weight: 30.0000 overall best weight: 7.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.130555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102635 restraints weight = 9011.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105358 restraints weight = 5294.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107070 restraints weight = 3716.564| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3392 Z= 0.244 Angle : 0.753 8.135 4614 Z= 0.386 Chirality : 0.047 0.158 497 Planarity : 0.004 0.046 601 Dihedral : 5.790 21.443 471 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.56 % Allowed : 28.41 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.41), residues: 424 helix: -3.56 (0.73), residues: 24 sheet: -0.28 (0.48), residues: 130 loop : -1.40 (0.38), residues: 270 =============================================================================== Job complete usr+sys time: 1017.11 seconds wall clock time: 19 minutes 8.57 seconds (1148.57 seconds total)