Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:13:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2022/7b6e_12053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2022/7b6e_12053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2022/7b6e_12053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2022/7b6e_12053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2022/7b6e_12053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2022/7b6e_12053.pdb" } resolution = 4.5 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= 0.003 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 358": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 2205 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2205 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 4, 'TRANS': 264} Chain breaks: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.77 Number of scatterers: 2205 At special positions: 0 Unit cell: (63.648, 73.632, 92.352, 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 13 16.00 O 397 8.00 N 389 7.00 C 1406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.96 Conformation dependent library (CDL) restraints added in 404.5 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 355 through 384 removed outlier: 4.194A pdb=" N HIS A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 425 through 438 removed outlier: 4.158A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 456 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 483 through 500 removed outlier: 3.762A pdb=" N THR A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 removed outlier: 4.176A pdb=" N ALA A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.905A pdb=" N ASN A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.726A pdb=" N THR A 556 " --> pdb=" O CYS A 552 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 579 removed outlier: 4.874A pdb=" N ARG A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.665A pdb=" N ARG A 598 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 4.015A pdb=" N GLU A 604 " --> pdb=" O TRP A 600 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 4.487A pdb=" N ALA A 624 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 165 hydrogen bonds defined for protein. 495 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: 0.49 Time building geometry restraints manager: 1.05 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: 691 1.34 - 1.46: 378 1.46 - 1.57: 1162 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 2252 Sorted by residual: bond pdb=" CB PRO A 559 " pdb=" CG PRO A 559 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.59e+00 bond pdb=" CG PRO A 559 " pdb=" CD PRO A 559 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" CB PHE A 436 " pdb=" CG PHE A 436 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.30e+00 bond pdb=" N TRP A 600 " pdb=" CA TRP A 600 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.20e+00 bond pdb=" CG LEU A 468 " pdb=" CD2 LEU A 468 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 ... (remaining 2247 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.31: 21 104.31 - 111.73: 947 111.73 - 119.14: 834 119.14 - 126.56: 1211 126.56 - 133.97: 24 Bond angle restraints: 3037 Sorted by residual: angle pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" CD PRO A 559 " ideal model delta sigma weight residual 112.00 102.11 9.89 1.40e+00 5.10e-01 4.99e+01 angle pdb=" C LEU A 434 " pdb=" N TYR A 435 " pdb=" CA TYR A 435 " ideal model delta sigma weight residual 121.58 113.58 8.00 1.95e+00 2.63e-01 1.68e+01 angle pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sigma weight residual 116.30 130.26 -13.96 3.50e+00 8.16e-02 1.59e+01 angle pdb=" CA ARG A 508 " pdb=" CB ARG A 508 " pdb=" CG ARG A 508 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" C ALA A 467 " pdb=" N LEU A 468 " pdb=" CA LEU A 468 " ideal model delta sigma weight residual 120.31 115.02 5.29 1.52e+00 4.33e-01 1.21e+01 ... (remaining 3032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 1143 15.16 - 30.32: 169 30.32 - 45.48: 35 45.48 - 60.64: 2 60.64 - 75.79: 4 Dihedral angle restraints: 1353 sinusoidal: 544 harmonic: 809 Sorted by residual: dihedral pdb=" CA ARG A 598 " pdb=" C ARG A 598 " pdb=" N GLU A 599 " pdb=" CA GLU A 599 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA SER A 538 " pdb=" C SER A 538 " pdb=" N ASP A 539 " pdb=" CA ASP A 539 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN A 482 " pdb=" C GLN A 482 " pdb=" N ARG A 483 " pdb=" CA ARG A 483 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 199 0.041 - 0.082: 93 0.082 - 0.123: 23 0.123 - 0.165: 6 0.165 - 0.206: 5 Chirality restraints: 326 Sorted by residual: chirality pdb=" CA GLN A 529 " pdb=" N GLN A 529 " pdb=" C GLN A 529 " pdb=" CB GLN A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG A 508 " pdb=" N ARG A 508 " pdb=" C ARG A 508 " pdb=" CB ARG A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU A 469 " pdb=" N GLU A 469 " pdb=" C GLU A 469 " pdb=" CB GLU A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 323 not shown) Planarity restraints: 388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 558 " 0.075 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 559 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 559 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 559 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 547 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" CD GLU A 547 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 547 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 547 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 508 " -0.039 9.50e-02 1.11e+02 2.36e-02 3.33e+00 pdb=" NE ARG A 508 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 508 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 508 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 508 " 0.009 2.00e-02 2.50e+03 ... (remaining 385 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 90 2.68 - 3.24: 2676 3.24 - 3.79: 3824 3.79 - 4.35: 5131 4.35 - 4.90: 7212 Nonbonded interactions: 18933 Sorted by model distance: nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 474 " model vdw 2.129 2.440 nonbonded pdb=" OE1 GLN A 482 " pdb=" NZ LYS A 484 " model vdw 2.161 2.520 nonbonded pdb=" O CYS A 516 " pdb=" OG1 THR A 519 " model vdw 2.178 2.440 nonbonded pdb=" O GLU A 382 " pdb=" OG1 THR A 385 " model vdw 2.191 2.440 nonbonded pdb=" O ALA A 612 " pdb=" N TYR A 616 " model vdw 2.203 2.520 ... (remaining 18928 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 13 5.16 5 C 1406 2.51 5 N 389 2.21 5 O 397 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: 0.010 Normalize map: mean=0, sd=1: 3.430 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: 13.390 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.010 Process input model: 12.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 : 0.005 0.063 2252 Z= 0.309 Angle : 1.026 13.963 3037 Z= 0.575 Chirality : 0.053 0.206 326 Planarity : 0.007 0.108 388 Dihedral : 15.044 75.794 831 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 36.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.88 (0.43), residues: 265 helix: -2.02 (0.29), residues: 225 sheet: None (None), residues: 0 loop : -4.52 (0.69), residues: 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1871 time to fit residues: 6.5788 Evaluate side-chains 24 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2252 Z= 0.223 Angle : 0.873 12.479 3037 Z= 0.447 Chirality : 0.047 0.173 326 Planarity : 0.005 0.042 388 Dihedral : 6.947 25.726 306 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.46), residues: 265 helix: -1.27 (0.31), residues: 224 sheet: None (None), residues: 0 loop : -4.38 (0.68), residues: 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1990 time to fit residues: 7.3809 Evaluate side-chains 23 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 2252 Z= 0.234 Angle : 0.895 13.401 3037 Z= 0.456 Chirality : 0.046 0.185 326 Planarity : 0.005 0.039 388 Dihedral : 6.790 26.331 306 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.46), residues: 265 helix: -1.06 (0.31), residues: 224 sheet: None (None), residues: 0 loop : -4.24 (0.68), residues: 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2203 time to fit residues: 8.3537 Evaluate side-chains 25 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2252 Z= 0.220 Angle : 0.878 13.891 3037 Z= 0.441 Chirality : 0.045 0.179 326 Planarity : 0.004 0.038 388 Dihedral : 6.559 24.682 306 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.47), residues: 265 helix: -0.81 (0.32), residues: 223 sheet: None (None), residues: 0 loop : -4.23 (0.67), residues: 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.303 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2090 time to fit residues: 7.9402 Evaluate side-chains 26 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- 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: 0.6585 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 2252 Z= 0.224 Angle : 0.865 13.701 3037 Z= 0.436 Chirality : 0.044 0.169 326 Planarity : 0.004 0.036 388 Dihedral : 6.550 24.461 306 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 28.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.48), residues: 265 helix: -0.73 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -4.15 (0.67), residues: 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2095 time to fit residues: 8.1006 Evaluate side-chains 27 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2252 Z= 0.213 Angle : 0.866 14.444 3037 Z= 0.430 Chirality : 0.045 0.166 326 Planarity : 0.004 0.036 388 Dihedral : 6.418 23.416 306 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.49), residues: 265 helix: -0.47 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -4.21 (0.66), residues: 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1844 time to fit residues: 7.4076 Evaluate side-chains 28 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.6556 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 2252 Z= 0.214 Angle : 0.864 14.714 3037 Z= 0.426 Chirality : 0.044 0.163 326 Planarity : 0.004 0.034 388 Dihedral : 6.319 23.329 306 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.49), residues: 265 helix: -0.33 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -4.32 (0.65), residues: 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2190 time to fit residues: 8.9531 Evaluate side-chains 29 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.6556 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 2252 Z= 0.229 Angle : 0.904 15.921 3037 Z= 0.448 Chirality : 0.047 0.176 326 Planarity : 0.004 0.033 388 Dihedral : 6.351 22.853 306 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.50), residues: 265 helix: -0.37 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -4.34 (0.64), residues: 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.306 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1970 time to fit residues: 8.4141 Evaluate side-chains 29 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.6548 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 2252 Z= 0.277 Angle : 0.995 17.636 3037 Z= 0.501 Chirality : 0.048 0.169 326 Planarity : 0.004 0.032 388 Dihedral : 6.441 25.763 306 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.49), residues: 265 helix: -0.40 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -4.18 (0.66), residues: 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.282 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2034 time to fit residues: 8.2189 Evaluate side-chains 29 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.6518 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 2252 Z= 0.225 Angle : 0.951 17.918 3037 Z= 0.469 Chirality : 0.047 0.169 326 Planarity : 0.004 0.032 388 Dihedral : 6.303 22.697 306 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.50), residues: 265 helix: -0.19 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -4.18 (0.67), residues: 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2024 time to fit residues: 7.9820 Evaluate side-chains 28 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.076931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.066008 restraints weight = 20429.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.067398 restraints weight = 13927.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.068456 restraints weight = 10177.550| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2252 Z= 0.223 Angle : 0.945 17.648 3037 Z= 0.472 Chirality : 0.046 0.182 326 Planarity : 0.004 0.031 388 Dihedral : 6.231 21.737 306 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.50), residues: 265 helix: -0.09 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -4.23 (0.66), residues: 48 =============================================================================== Job complete usr+sys time: 990.45 seconds wall clock time: 18 minutes 46.69 seconds (1126.69 seconds total)