Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:25:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/11_2022/7swn_25476_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/11_2022/7swn_25476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/11_2022/7swn_25476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/11_2022/7swn_25476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/11_2022/7swn_25476_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/11_2022/7swn_25476_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Time building chain proxies: 2.47, per 1000 atoms: 0.75 Number of scatterers: 3283 At special positions: 0 Unit cell: (100.65, 70.95, 75.075, 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 17 16.00 O 632 8.00 N 554 7.00 C 2080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 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: 1.26 Conformation dependent library (CDL) restraints added in 461.0 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.3% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.034A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.551A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.319A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.864A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.864A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 102 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.398A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA9, first strand: chain 'L' and resid 20 through 23 83 hydrogen bonds defined for protein. 186 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: 0.81 Time building geometry restraints manager: 1.38 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: 1043 1.34 - 1.46: 862 1.46 - 1.58: 1442 1.58 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 3367 Sorted by residual: bond pdb=" N VAL H 67 " pdb=" CA VAL H 67 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.22e+00 bond pdb=" N VAL H 89 " pdb=" CA VAL H 89 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.12e+00 bond pdb=" N VAL L 104 " pdb=" CA VAL L 104 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.79e+00 bond pdb=" N ARG H 71 " pdb=" CA ARG H 71 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.29e-02 6.01e+03 7.54e+00 bond pdb=" N ASN A 450 " pdb=" CA ASN A 450 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 7.12e+00 ... (remaining 3362 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.15: 66 105.15 - 112.62: 1676 112.62 - 120.10: 1265 120.10 - 127.57: 1536 127.57 - 135.04: 34 Bond angle restraints: 4577 Sorted by residual: angle pdb=" N VAL H 89 " pdb=" CA VAL H 89 " pdb=" C VAL H 89 " ideal model delta sigma weight residual 106.88 97.68 9.20 1.52e+00 4.33e-01 3.66e+01 angle pdb=" N PRO L 59 " pdb=" CA PRO L 59 " pdb=" C PRO L 59 " ideal model delta sigma weight residual 111.15 118.00 -6.85 1.58e+00 4.01e-01 1.88e+01 angle pdb=" C ILE L 58 " pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 119.90 124.22 -4.32 1.02e+00 9.61e-01 1.80e+01 angle pdb=" N SER H 74 " pdb=" CA SER H 74 " pdb=" C SER H 74 " ideal model delta sigma weight residual 112.68 107.38 5.30 1.33e+00 5.65e-01 1.59e+01 angle pdb=" N ARG L 61 " pdb=" CA ARG L 61 " pdb=" C ARG L 61 " ideal model delta sigma weight residual 113.31 105.45 7.86 2.04e+00 2.40e-01 1.48e+01 ... (remaining 4572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 1754 16.34 - 32.68: 182 32.68 - 49.01: 42 49.01 - 65.35: 8 65.35 - 81.69: 4 Dihedral angle restraints: 1990 sinusoidal: 771 harmonic: 1219 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -127.47 41.47 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CA VAL A 401 " pdb=" C VAL A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ALA A 522 " pdb=" C ALA A 522 " pdb=" N THR A 523 " pdb=" CA THR A 523 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 1987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 407 0.072 - 0.144: 78 0.144 - 0.216: 6 0.216 - 0.288: 0 0.288 - 0.360: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL H 89 " pdb=" N VAL H 89 " pdb=" C VAL H 89 " pdb=" CB VAL H 89 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA VAL L 104 " pdb=" N VAL L 104 " pdb=" C VAL L 104 " pdb=" CB VAL L 104 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL A 407 " pdb=" CA VAL A 407 " pdb=" CG1 VAL A 407 " pdb=" CG2 VAL A 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 489 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 100F" 0.023 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE H 100F" -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE H 100F" 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE H 100F" 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE H 100F" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 100F" 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE H 100F" -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP H 50 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 426 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.032 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 478 2.74 - 3.28: 3571 3.28 - 3.82: 5496 3.82 - 4.36: 6691 4.36 - 4.90: 10807 Nonbonded interactions: 27043 Sorted by model distance: nonbonded pdb=" O LEU L 4 " pdb=" NE2 GLN L 100 " model vdw 2.203 2.520 nonbonded pdb=" OH TYR A 451 " pdb=" O PHE A 497 " model vdw 2.205 2.440 nonbonded pdb=" O LYS H 12 " pdb=" N SER H 112 " model vdw 2.210 2.520 nonbonded pdb=" O PHE H 63 " pdb=" CG1 VAL H 67 " model vdw 2.238 3.460 nonbonded pdb=" O LYS H 62 " pdb=" NH2 ARG H 66 " model vdw 2.241 2.520 ... (remaining 27038 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2080 2.51 5 N 554 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.960 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 14.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.007 0.069 3367 Z= 0.482 Angle : 1.064 10.040 4577 Z= 0.608 Chirality : 0.058 0.360 492 Planarity : 0.007 0.058 592 Dihedral : 14.582 81.689 1195 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 41.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.88 % Favored : 78.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.82 (0.35), residues: 416 helix: -4.85 (0.38), residues: 30 sheet: -2.02 (0.52), residues: 102 loop : -3.75 (0.30), residues: 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2076 time to fit residues: 23.9802 Evaluate side-chains 68 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5169 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3367 Z= 0.234 Angle : 0.768 9.369 4577 Z= 0.395 Chirality : 0.047 0.150 492 Planarity : 0.006 0.048 592 Dihedral : 6.339 23.235 466 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.35 (0.35), residues: 416 helix: -4.53 (0.50), residues: 24 sheet: -1.62 (0.49), residues: 100 loop : -3.48 (0.31), residues: 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1773 time to fit residues: 21.1240 Evaluate side-chains 71 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 474 GLN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 3367 Z= 0.308 Angle : 0.796 10.201 4577 Z= 0.407 Chirality : 0.048 0.155 492 Planarity : 0.007 0.048 592 Dihedral : 6.427 20.563 466 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.33 (0.36), residues: 416 helix: -4.36 (0.53), residues: 24 sheet: -1.73 (0.49), residues: 100 loop : -3.42 (0.31), residues: 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1676 time to fit residues: 18.7215 Evaluate side-chains 63 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3367 Z= 0.263 Angle : 0.755 9.290 4577 Z= 0.385 Chirality : 0.047 0.162 492 Planarity : 0.006 0.047 592 Dihedral : 6.116 25.190 466 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.15 (0.35), residues: 416 helix: -4.20 (0.60), residues: 24 sheet: -1.53 (0.51), residues: 90 loop : -3.30 (0.31), residues: 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1791 time to fit residues: 20.3013 Evaluate side-chains 65 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0526 time to fit residues: 0.5367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.0040 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3367 Z= 0.190 Angle : 0.706 8.995 4577 Z= 0.355 Chirality : 0.045 0.155 492 Planarity : 0.005 0.045 592 Dihedral : 5.367 17.111 466 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.89 (0.36), residues: 416 helix: -4.02 (0.63), residues: 24 sheet: -1.39 (0.50), residues: 95 loop : -3.12 (0.31), residues: 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1571 time to fit residues: 19.3540 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.392 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.0000 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 3367 Z= 0.463 Angle : 0.916 9.826 4577 Z= 0.478 Chirality : 0.050 0.203 492 Planarity : 0.007 0.052 592 Dihedral : 6.799 19.721 466 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 40.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.31 % Favored : 82.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.22 (0.35), residues: 416 helix: -4.34 (0.50), residues: 24 sheet: -1.75 (0.48), residues: 100 loop : -3.30 (0.30), residues: 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1549 time to fit residues: 15.9093 Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3367 Z= 0.225 Angle : 0.741 8.935 4577 Z= 0.371 Chirality : 0.047 0.153 492 Planarity : 0.005 0.046 592 Dihedral : 5.803 18.689 466 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.83 (0.35), residues: 416 helix: -4.22 (0.54), residues: 24 sheet: -1.35 (0.51), residues: 98 loop : -3.06 (0.31), residues: 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1515 time to fit residues: 17.5567 Evaluate side-chains 77 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3367 Z= 0.300 Angle : 0.798 9.393 4577 Z= 0.404 Chirality : 0.047 0.149 492 Planarity : 0.006 0.048 592 Dihedral : 6.079 18.280 466 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.83 (0.35), residues: 416 helix: -4.24 (0.57), residues: 24 sheet: -1.44 (0.50), residues: 94 loop : -3.00 (0.31), residues: 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1362 time to fit residues: 16.6302 Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.0040 chunk 37 optimal weight: 4.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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: 0.6647 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 3367 Z= 0.215 Angle : 0.757 8.925 4577 Z= 0.382 Chirality : 0.048 0.171 492 Planarity : 0.006 0.046 592 Dihedral : 5.761 17.873 466 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.65 (0.36), residues: 416 helix: -4.58 (0.50), residues: 24 sheet: -1.39 (0.48), residues: 103 loop : -2.83 (0.32), residues: 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1360 time to fit residues: 17.4289 Evaluate side-chains 77 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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: 0.6633 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3367 Z= 0.207 Angle : 0.737 8.986 4577 Z= 0.368 Chirality : 0.046 0.149 492 Planarity : 0.006 0.049 592 Dihedral : 5.536 18.809 466 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.68 (0.37), residues: 416 helix: -4.44 (0.44), residues: 30 sheet: -1.21 (0.49), residues: 102 loop : -2.89 (0.33), residues: 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1415 time to fit residues: 17.9582 Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.088122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.075720 restraints weight = 15250.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078089 restraints weight = 9740.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.079846 restraints weight = 6865.321| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3367 Z= 0.258 Angle : 0.790 8.993 4577 Z= 0.394 Chirality : 0.047 0.180 492 Planarity : 0.006 0.051 592 Dihedral : 5.784 18.054 466 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.79 (0.36), residues: 416 helix: -4.53 (0.39), residues: 30 sheet: -1.33 (0.50), residues: 99 loop : -2.94 (0.33), residues: 287 =============================================================================== Job complete usr+sys time: 1162.48 seconds wall clock time: 21 minutes 56.56 seconds (1316.56 seconds total)