Starting phenix.real_space_refine (version: dev) on Sun Dec 11 16:43:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/12_2022/7slq_25198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/12_2022/7slq_25198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/12_2022/7slq_25198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/12_2022/7slq_25198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/12_2022/7slq_25198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/12_2022/7slq_25198_updated.pdb" } resolution = 3.7 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= 0.005 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 433": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B ARG 565": "NH1" <-> "NH2" 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: 5451 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1862 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2473 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1090 Unusual residues: {'G5J': 1} Classifications: {'RNA': 50, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 37, None: 1} Not linked: pdbres="G5J R 1 " pdbres=" G R 2 " Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.67 Number of scatterers: 5451 At special positions: 0 Unit cell: (82.39, 92.02, 103.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 53 15.00 O 1157 8.00 N 958 7.00 C 3269 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 647.2 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 4 sheets defined 41.3% alpha, 11.8% beta 13 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 458 through 464 removed outlier: 4.008A pdb=" N LYS A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.852A pdb=" N HIS A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.793A pdb=" N SER A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 584 through 606 removed outlier: 7.969A pdb=" N ASP A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLU A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 626 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.586A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 412 Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 553 through 570 Processing sheet with id= A, first strand: chain 'A' and resid 660 through 663 removed outlier: 3.511A pdb=" N SER A 660 " --> pdb=" O HIS A 682 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 616 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 581 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A 469 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASP A 449 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 471 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 554 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP A 474 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 556 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.673A pdb=" N VAL B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.558A pdb=" N ARG B 377 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 519 through 523 166 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1016 1.33 - 1.45: 1622 1.45 - 1.57: 2902 1.57 - 1.69: 106 1.69 - 1.81: 22 Bond restraints: 5668 Sorted by residual: bond pdb=" C3' G5J R 1 " pdb=" O3' G5J R 1 " ideal model delta sigma weight residual 1.404 1.737 -0.333 2.00e-02 2.50e+03 2.78e+02 bond pdb=" C3' G5J R 1 " pdb=" C4' G5J R 1 " ideal model delta sigma weight residual 1.526 1.248 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C1' G5J R 1 " pdb=" C2' G5J R 1 " ideal model delta sigma weight residual 1.524 1.254 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C6 G5J R 1 " pdb=" O6 G5J R 1 " ideal model delta sigma weight residual 1.226 1.433 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C2' G5J R 1 " pdb=" C3' G5J R 1 " ideal model delta sigma weight residual 1.531 1.722 -0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 5663 not shown) Histogram of bond angle deviations from ideal: 91.52 - 101.07: 19 101.07 - 110.62: 2058 110.62 - 120.17: 3512 120.17 - 129.72: 2277 129.72 - 139.28: 58 Bond angle restraints: 7924 Sorted by residual: angle pdb=" C VAL B 99 " pdb=" N VAL B 100 " pdb=" CA VAL B 100 " ideal model delta sigma weight residual 121.97 128.13 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" O3' A R 298 " pdb=" C3' A R 298 " pdb=" C2' A R 298 " ideal model delta sigma weight residual 109.50 118.39 -8.89 1.50e+00 4.44e-01 3.51e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " ideal model delta sigma weight residual 111.05 102.42 8.63 1.50e+00 4.44e-01 3.31e+01 angle pdb=" O3A G5J R 1 " pdb=" PB G5J R 1 " pdb=" O3B G5J R 1 " ideal model delta sigma weight residual 92.82 109.77 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 117.58 -8.18 1.50e+00 4.44e-01 2.98e+01 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 3168 34.50 - 69.00: 79 69.00 - 103.50: 7 103.50 - 138.00: 1 138.00 - 172.50: 2 Dihedral angle restraints: 3257 sinusoidal: 1628 harmonic: 1629 Sorted by residual: dihedral pdb=" C5' A R 298 " pdb=" C4' A R 298 " pdb=" C3' A R 298 " pdb=" O3' A R 298 " ideal model delta sinusoidal sigma weight residual 147.00 105.99 41.01 1 8.00e+00 1.56e-02 3.68e+01 dihedral pdb=" CA ASN B 135 " pdb=" C ASN B 135 " pdb=" N VAL B 136 " pdb=" CA VAL B 136 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" O4' A R 296 " pdb=" C1' A R 296 " pdb=" N9 A R 296 " pdb=" C4 A R 296 " ideal model delta sinusoidal sigma weight residual -106.00 -171.42 65.42 1 1.70e+01 3.46e-03 1.94e+01 ... (remaining 3254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 875 0.118 - 0.237: 54 0.237 - 0.355: 2 0.355 - 0.473: 2 0.473 - 0.591: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" C3' A R 298 " pdb=" C4' A R 298 " pdb=" O3' A R 298 " pdb=" C2' A R 298 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" C PRO A 427 " pdb=" CB PRO A 427 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' G5J R 1 " pdb=" C2' G5J R 1 " pdb=" C4' G5J R 1 " pdb=" O3' G5J R 1 " both_signs ideal model delta sigma weight residual False -2.71 -3.10 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 931 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 549 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO A 550 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G5J R 1 " -0.031 2.00e-02 2.50e+03 1.47e-02 6.50e+00 pdb=" C2 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" C8 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G5J R 1 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G5J R 1 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G5J R 1 " 0.026 2.00e-02 2.50e+03 pdb=" N9 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G5J R 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 132 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO B 133 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 185 2.69 - 3.25: 4874 3.25 - 3.80: 8785 3.80 - 4.35: 10870 4.35 - 4.90: 17241 Nonbonded interactions: 41955 Sorted by model distance: nonbonded pdb=" O2' A R 297 " pdb=" OP1 A R 298 " model vdw 2.144 2.440 nonbonded pdb=" O GLY A 532 " pdb=" OH TYR B 391 " model vdw 2.239 2.440 nonbonded pdb=" O SER B 461 " pdb=" OG1 THR B 491 " model vdw 2.331 2.440 nonbonded pdb=" O TYR A 650 " pdb=" OG SER A 653 " model vdw 2.337 2.440 nonbonded pdb=" OD1 ASP A 474 " pdb=" O2' SAH A 701 " model vdw 2.341 2.440 ... (remaining 41950 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: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 14 5.16 5 C 3269 2.51 5 N 958 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 2.230 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.011 0.333 5668 Z= 0.790 Angle : 1.161 16.945 7924 Z= 0.628 Chirality : 0.062 0.591 934 Planarity : 0.007 0.069 815 Dihedral : 14.972 172.502 2203 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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 (0.30), residues: 546 helix: -2.16 (0.25), residues: 252 sheet: -0.52 (0.63), residues: 64 loop : -1.76 (0.35), residues: 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 109 average time/residue: 0.2238 time to fit residues: 29.9037 Evaluate side-chains 55 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1862 time to fit residues: 1.1953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0570 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN B 528 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 5668 Z= 0.160 Angle : 0.563 7.460 7924 Z= 0.292 Chirality : 0.038 0.192 934 Planarity : 0.005 0.080 815 Dihedral : 15.058 173.793 1209 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.49 (0.32), residues: 546 helix: -0.69 (0.30), residues: 257 sheet: -0.05 (0.75), residues: 47 loop : -1.40 (0.35), residues: 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.1896 time to fit residues: 16.9209 Evaluate side-chains 54 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1043 time to fit residues: 1.7788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 HIS B 33 GLN B 514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 5668 Z= 0.306 Angle : 0.648 6.882 7924 Z= 0.335 Chirality : 0.041 0.189 934 Planarity : 0.005 0.078 815 Dihedral : 14.955 174.464 1209 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.34), residues: 546 helix: -0.00 (0.32), residues: 250 sheet: 0.48 (0.74), residues: 52 loop : -1.42 (0.36), residues: 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 59 average time/residue: 0.1675 time to fit residues: 13.3386 Evaluate side-chains 51 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0567 time to fit residues: 1.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 514 ASN B 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5668 Z= 0.163 Angle : 0.540 6.822 7924 Z= 0.277 Chirality : 0.037 0.161 934 Planarity : 0.004 0.080 815 Dihedral : 14.629 176.271 1209 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 546 helix: 0.51 (0.33), residues: 249 sheet: 0.19 (0.77), residues: 47 loop : -1.22 (0.37), residues: 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 61 average time/residue: 0.1711 time to fit residues: 13.9913 Evaluate side-chains 47 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0654 time to fit residues: 1.1897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.7228 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 5668 Z= 0.277 Angle : 0.614 8.083 7924 Z= 0.312 Chirality : 0.039 0.173 934 Planarity : 0.005 0.082 815 Dihedral : 14.654 175.436 1209 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.35), residues: 546 helix: 0.41 (0.33), residues: 249 sheet: 0.37 (0.73), residues: 54 loop : -1.33 (0.37), residues: 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.568 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.1519 time to fit residues: 11.2653 Evaluate side-chains 47 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0557 time to fit residues: 1.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.0050 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.0670 chunk 42 optimal weight: 0.6980 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 41 GLN B 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5668 Z= 0.139 Angle : 0.524 8.077 7924 Z= 0.264 Chirality : 0.036 0.147 934 Planarity : 0.004 0.081 815 Dihedral : 14.348 176.732 1209 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.35), residues: 546 helix: 0.81 (0.34), residues: 248 sheet: 0.19 (0.77), residues: 49 loop : -1.13 (0.37), residues: 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.533 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.1749 time to fit residues: 13.4506 Evaluate side-chains 48 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0712 time to fit residues: 1.5736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.0050 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN B 33 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5668 Z= 0.145 Angle : 0.505 9.132 7924 Z= 0.254 Chirality : 0.036 0.154 934 Planarity : 0.005 0.089 815 Dihedral : 14.211 175.179 1209 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.36), residues: 546 helix: 0.86 (0.33), residues: 248 sheet: 0.38 (0.70), residues: 58 loop : -1.11 (0.38), residues: 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.561 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.1341 time to fit residues: 9.3141 Evaluate side-chains 39 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.0070 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5668 Z= 0.185 Angle : 0.516 5.603 7924 Z= 0.266 Chirality : 0.037 0.146 934 Planarity : 0.005 0.089 815 Dihedral : 14.202 174.668 1209 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.36), residues: 546 helix: 0.80 (0.34), residues: 247 sheet: 0.31 (0.71), residues: 56 loop : -1.10 (0.38), residues: 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.586 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.1484 time to fit residues: 10.0103 Evaluate side-chains 40 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0705 time to fit residues: 1.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5668 Z= 0.186 Angle : 0.540 10.193 7924 Z= 0.274 Chirality : 0.036 0.149 934 Planarity : 0.005 0.093 815 Dihedral : 14.189 174.378 1209 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.35), residues: 546 helix: 0.75 (0.33), residues: 247 sheet: 0.27 (0.71), residues: 56 loop : -1.12 (0.38), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.588 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1718 time to fit residues: 11.2179 Evaluate side-chains 40 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0543 time to fit residues: 0.8760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 5668 Z= 0.298 Angle : 0.632 8.718 7924 Z= 0.326 Chirality : 0.040 0.159 934 Planarity : 0.006 0.095 815 Dihedral : 14.371 173.964 1209 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.35), residues: 546 helix: 0.41 (0.33), residues: 247 sheet: 0.54 (0.70), residues: 59 loop : -1.30 (0.37), residues: 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.625 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1712 time to fit residues: 10.2067 Evaluate side-chains 38 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0675 time to fit residues: 0.8803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0050 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 chunk 1 optimal weight: 0.0570 chunk 38 optimal weight: 9.9990 overall best weight: 0.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.174291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135448 restraints weight = 9593.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.136533 restraints weight = 9180.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138301 restraints weight = 7764.749| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5668 Z= 0.138 Angle : 0.513 6.984 7924 Z= 0.264 Chirality : 0.035 0.142 934 Planarity : 0.005 0.092 815 Dihedral : 14.092 174.953 1209 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.36), residues: 546 helix: 0.93 (0.34), residues: 240 sheet: 0.59 (0.68), residues: 56 loop : -0.99 (0.38), residues: 250 =============================================================================== Job complete usr+sys time: 1144.61 seconds wall clock time: 21 minutes 29.08 seconds (1289.08 seconds total)