Starting phenix.real_space_refine (version: dev) on Fri Feb 17 03:38:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/02_2023/7swn_25476_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/02_2023/7swn_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_25476/02_2023/7swn_25476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/02_2023/7swn_25476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/02_2023/7swn_25476_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/02_2023/7swn_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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 2.33, per 1000 atoms: 0.71 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: 1.11 Conformation dependent library (CDL) restraints added in 393.7 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: 0.88 Time building geometry restraints manager: 1.23 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: 1.350 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: 2.720 Check model and map are aligned: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- 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 : 0.405 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: 0.2265 time to fit residues: 26.0465 Evaluate side-chains 68 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5177 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.6724 moved from start: 0.2693 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= 0.239 Angle : 0.774 9.446 4577 Z= 0.397 Chirality : 0.047 0.151 492 Planarity : 0.006 0.048 592 Dihedral : 6.404 22.930 466 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % 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: -4.28 (0.35), residues: 416 helix: -4.55 (0.50), residues: 24 sheet: -1.53 (0.51), residues: 95 loop : -3.42 (0.30), residues: 297 *********************** 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 99 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.565 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: 99 average time/residue: 0.1950 time to fit residues: 22.6470 Evaluate side-chains 69 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4795 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 3367 Z= 0.300 Angle : 0.791 10.000 4577 Z= 0.405 Chirality : 0.048 0.146 492 Planarity : 0.007 0.047 592 Dihedral : 6.454 20.557 466 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 31.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.14 % Favored : 84.86 % 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 (0.35), residues: 416 helix: -4.40 (0.52), residues: 24 sheet: -1.74 (0.48), 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 93 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2040 time to fit residues: 22.5189 Evaluate side-chains 61 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5030 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 3367 Z= 0.302 Angle : 0.794 9.629 4577 Z= 0.407 Chirality : 0.048 0.155 492 Planarity : 0.006 0.043 592 Dihedral : 6.412 26.975 466 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 28.65 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: -4.37 (0.35), residues: 416 helix: -4.30 (0.55), residues: 24 sheet: -1.87 (0.48), residues: 97 loop : -3.41 (0.31), residues: 295 *********************** 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: 0 poor density : 95 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1961 time to fit residues: 21.8497 Evaluate side-chains 63 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6191 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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: 0.6801 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 3367 Z= 0.264 Angle : 0.772 9.411 4577 Z= 0.393 Chirality : 0.046 0.153 492 Planarity : 0.006 0.045 592 Dihedral : 6.111 22.072 466 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % 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: -4.11 (0.36), residues: 416 helix: -4.23 (0.58), residues: 24 sheet: -1.54 (0.50), residues: 95 loop : -3.27 (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 96 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.1723 time to fit residues: 19.8239 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0378 time to fit residues: 0.5838 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 3367 Z= 0.328 Angle : 0.828 9.391 4577 Z= 0.422 Chirality : 0.047 0.151 492 Planarity : 0.006 0.053 592 Dihedral : 6.498 24.388 466 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: -4.15 (0.35), residues: 416 helix: -4.52 (0.40), residues: 24 sheet: -1.51 (0.50), residues: 96 loop : -3.30 (0.31), residues: 296 *********************** 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 91 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1479 time to fit residues: 16.4267 Evaluate side-chains 64 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4606 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3367 Z= 0.259 Angle : 0.787 9.102 4577 Z= 0.397 Chirality : 0.047 0.155 492 Planarity : 0.006 0.054 592 Dihedral : 6.176 21.189 466 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % 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: -3.92 (0.36), residues: 416 helix: -4.31 (0.53), residues: 24 sheet: -1.36 (0.52), residues: 92 loop : -3.11 (0.32), residues: 300 *********************** 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 91 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 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: 91 average time/residue: 0.1533 time to fit residues: 17.2032 Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5561 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3367 Z= 0.214 Angle : 0.762 9.097 4577 Z= 0.383 Chirality : 0.046 0.149 492 Planarity : 0.006 0.054 592 Dihedral : 5.838 19.170 466 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % 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: -3.80 (0.36), residues: 416 helix: -4.47 (0.61), residues: 18 sheet: -1.36 (0.50), residues: 95 loop : -3.03 (0.31), residues: 303 *********************** 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 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1522 time to fit residues: 17.5776 Evaluate side-chains 68 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5242 ------------------------------------------------------------------------------- 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: 0.8980 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 0.0030 chunk 27 optimal weight: 0.0370 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3367 Z= 0.195 Angle : 0.762 8.716 4577 Z= 0.383 Chirality : 0.048 0.184 492 Planarity : 0.006 0.054 592 Dihedral : 5.502 19.427 466 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % 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: -3.64 (0.36), residues: 416 helix: -4.53 (0.53), residues: 24 sheet: -1.12 (0.50), residues: 93 loop : -2.89 (0.32), residues: 299 *********************** 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 103 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1585 time to fit residues: 19.9781 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5695 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3367 Z= 0.182 Angle : 0.732 8.435 4577 Z= 0.365 Chirality : 0.046 0.174 492 Planarity : 0.006 0.051 592 Dihedral : 5.333 20.708 466 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % 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: -3.41 (0.37), residues: 416 helix: -4.45 (0.56), residues: 24 sheet: -1.13 (0.47), residues: 114 loop : -2.73 (0.34), residues: 278 ********************** 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 : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1951 time to fit residues: 24.4747 Evaluate side-chains 70 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4690 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.079915 restraints weight = 15141.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.082506 restraints weight = 9371.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084356 restraints weight = 6418.485| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3367 Z= 0.204 Angle : 0.738 8.505 4577 Z= 0.369 Chirality : 0.046 0.182 492 Planarity : 0.006 0.052 592 Dihedral : 5.323 18.745 466 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 21.52 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: -3.20 (0.38), residues: 416 helix: -4.39 (0.58), residues: 24 sheet: -0.94 (0.49), residues: 110 loop : -2.58 (0.34), residues: 282 =============================================================================== Job complete usr+sys time: 1258.00 seconds wall clock time: 23 minutes 36.49 seconds (1416.49 seconds total)