Mon 24 Dec 00:24:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2awa-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:24:50 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1127 and 0 Target number of residues in the AU: 1127 Target solvent content: 0.6635 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-3.8-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.85 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 135.654 3.800 Wilson plot Bfac: 87.31 17103 reflections ( 95.07 % complete ) and 0 restraints for refining 13781 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3510 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3166 (Rfree = 0.000) for 13781 atoms. Found 75 (75 requested) and removed 80 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 13929 seeds are put forward NCS extension: 0 residues added, 13929 seeds are put forward Round 1: 434 peptides, 93 chains. Longest chain 12 peptides. Score 0.239 Round 2: 576 peptides, 110 chains. Longest chain 11 peptides. Score 0.313 Round 3: 634 peptides, 118 chains. Longest chain 12 peptides. Score 0.336 Round 4: 692 peptides, 120 chains. Longest chain 20 peptides. Score 0.382 Round 5: 693 peptides, 120 chains. Longest chain 14 peptides. Score 0.383 Taking the results from Round 5 Chains 121, Residues 573, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 27193 restraints for refining 11282 atoms. 24994 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2508 (Rfree = 0.000) for 11282 atoms. Found 25 (62 requested) and removed 92 (31 requested) atoms. Cycle 2: After refmac, R = 0.2330 (Rfree = 0.000) for 11045 atoms. Found 38 (61 requested) and removed 52 (30 requested) atoms. Cycle 3: After refmac, R = 0.2174 (Rfree = 0.000) for 10959 atoms. Found 36 (60 requested) and removed 50 (30 requested) atoms. Cycle 4: After refmac, R = 0.2219 (Rfree = 0.000) for 10903 atoms. Found 38 (60 requested) and removed 52 (30 requested) atoms. Cycle 5: After refmac, R = 0.2045 (Rfree = 0.000) for 10852 atoms. Found 22 (59 requested) and removed 50 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 11124 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 11143 seeds are put forward Round 1: 599 peptides, 125 chains. Longest chain 9 peptides. Score 0.272 Round 2: 688 peptides, 120 chains. Longest chain 15 peptides. Score 0.378 Round 3: 715 peptides, 121 chains. Longest chain 13 peptides. Score 0.399 Round 4: 715 peptides, 110 chains. Longest chain 17 peptides. Score 0.441 Round 5: 676 peptides, 110 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 4 Chains 110, Residues 605, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26338 restraints for refining 11225 atoms. 24028 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2088 (Rfree = 0.000) for 11225 atoms. Found 33 (61 requested) and removed 95 (30 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2033 (Rfree = 0.000) for 11092 atoms. Found 25 (61 requested) and removed 59 (30 requested) atoms. Cycle 8: After refmac, R = 0.1733 (Rfree = 0.000) for 11010 atoms. Found 10 (60 requested) and removed 42 (30 requested) atoms. Cycle 9: After refmac, R = 0.1650 (Rfree = 0.000) for 10956 atoms. Found 1 (60 requested) and removed 34 (30 requested) atoms. Cycle 10: After refmac, R = 0.1632 (Rfree = 0.000) for 10913 atoms. Found 7 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 11159 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 11184 seeds are put forward Round 1: 672 peptides, 132 chains. Longest chain 12 peptides. Score 0.315 Round 2: 692 peptides, 117 chains. Longest chain 18 peptides. Score 0.394 Round 3: 735 peptides, 114 chains. Longest chain 16 peptides. Score 0.443 Round 4: 722 peptides, 119 chains. Longest chain 17 peptides. Score 0.413 Round 5: 755 peptides, 118 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 5 Chains 118, Residues 637, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26063 restraints for refining 11284 atoms. 23633 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2048 (Rfree = 0.000) for 11284 atoms. Found 45 (62 requested) and removed 66 (31 requested) atoms. Cycle 12: After refmac, R = 0.2017 (Rfree = 0.000) for 11209 atoms. Found 44 (61 requested) and removed 55 (30 requested) atoms. Cycle 13: After refmac, R = 0.1976 (Rfree = 0.000) for 11150 atoms. Found 42 (61 requested) and removed 50 (30 requested) atoms. Cycle 14: After refmac, R = 0.1901 (Rfree = 0.000) for 11106 atoms. Found 49 (61 requested) and removed 48 (30 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 11075 atoms. Found 35 (61 requested) and removed 51 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 11326 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11346 seeds are put forward Round 1: 660 peptides, 124 chains. Longest chain 13 peptides. Score 0.336 Round 2: 727 peptides, 119 chains. Longest chain 19 peptides. Score 0.417 Round 3: 763 peptides, 122 chains. Longest chain 19 peptides. Score 0.437 Round 4: 779 peptides, 121 chains. Longest chain 20 peptides. Score 0.454 Round 5: 742 peptides, 115 chains. Longest chain 19 peptides. Score 0.445 Taking the results from Round 4 Chains 121, Residues 658, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 25735 restraints for refining 11286 atoms. 23203 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1976 (Rfree = 0.000) for 11286 atoms. Found 33 (62 requested) and removed 60 (31 requested) atoms. Cycle 17: After refmac, R = 0.1846 (Rfree = 0.000) for 11199 atoms. Found 23 (61 requested) and removed 42 (30 requested) atoms. Cycle 18: After refmac, R = 0.1905 (Rfree = 0.000) for 11147 atoms. Found 40 (61 requested) and removed 44 (30 requested) atoms. Cycle 19: After refmac, R = 0.1828 (Rfree = 0.000) for 11113 atoms. Found 46 (61 requested) and removed 42 (30 requested) atoms. Cycle 20: After refmac, R = 0.1518 (Rfree = 0.000) for 11089 atoms. Found 12 (61 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 11284 seeds are put forward NCS extension: 47 residues added (1 deleted due to clashes), 11331 seeds are put forward Round 1: 629 peptides, 125 chains. Longest chain 12 peptides. Score 0.302 Round 2: 679 peptides, 117 chains. Longest chain 14 peptides. Score 0.382 Round 3: 697 peptides, 116 chains. Longest chain 13 peptides. Score 0.402 Round 4: 710 peptides, 124 chains. Longest chain 14 peptides. Score 0.383 Round 5: 715 peptides, 121 chains. Longest chain 15 peptides. Score 0.399 Taking the results from Round 3 Chains 116, Residues 581, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 17103 reflections ( 95.07 % complete ) and 26135 restraints for refining 11288 atoms. 23892 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2025 (Rfree = 0.000) for 11288 atoms. Found 38 (62 requested) and removed 52 (31 requested) atoms. Cycle 22: After refmac, R = 0.2034 (Rfree = 0.000) for 11198 atoms. Found 53 (62 requested) and removed 41 (31 requested) atoms. Cycle 23: After refmac, R = 0.1940 (Rfree = 0.000) for 11180 atoms. Found 57 (61 requested) and removed 44 (30 requested) atoms. Cycle 24: After refmac, R = 0.1891 (Rfree = 0.000) for 11169 atoms. Found 52 (61 requested) and removed 44 (30 requested) atoms. Cycle 25: After refmac, R = 0.1554 (Rfree = 0.000) for 11153 atoms. Found 10 (61 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 11369 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 11381 seeds are put forward Round 1: 546 peptides, 114 chains. Longest chain 12 peptides. Score 0.265 Round 2: 658 peptides, 120 chains. Longest chain 11 peptides. Score 0.350 Round 3: 681 peptides, 118 chains. Longest chain 16 peptides. Score 0.380 Round 4: 668 peptides, 113 chains. Longest chain 13 peptides. Score 0.388 Round 5: 675 peptides, 113 chains. Longest chain 17 peptides. Score 0.394 Taking the results from Round 5 Chains 113, Residues 562, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26448 restraints for refining 11288 atoms. 24313 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1939 (Rfree = 0.000) for 11288 atoms. Found 27 (62 requested) and removed 43 (31 requested) atoms. Cycle 27: After refmac, R = 0.2001 (Rfree = 0.000) for 11219 atoms. Found 55 (61 requested) and removed 45 (30 requested) atoms. Cycle 28: After refmac, R = 0.1991 (Rfree = 0.000) for 11187 atoms. Found 61 (61 requested) and removed 42 (30 requested) atoms. Cycle 29: After refmac, R = 0.1561 (Rfree = 0.000) for 11178 atoms. Found 14 (61 requested) and removed 35 (30 requested) atoms. Cycle 30: After refmac, R = 0.1457 (Rfree = 0.000) for 11133 atoms. Found 11 (61 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 11364 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 11386 seeds are put forward Round 1: 565 peptides, 116 chains. Longest chain 11 peptides. Score 0.276 Round 2: 644 peptides, 121 chains. Longest chain 11 peptides. Score 0.333 Round 3: 660 peptides, 112 chains. Longest chain 19 peptides. Score 0.384 Round 4: 652 peptides, 112 chains. Longest chain 13 peptides. Score 0.377 Round 5: 665 peptides, 115 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 3 Chains 112, Residues 548, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26213 restraints for refining 11288 atoms. 24109 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1912 (Rfree = 0.000) for 11288 atoms. Found 51 (62 requested) and removed 51 (31 requested) atoms. Cycle 32: After refmac, R = 0.1939 (Rfree = 0.000) for 11239 atoms. Found 57 (62 requested) and removed 47 (31 requested) atoms. Cycle 33: After refmac, R = 0.1519 (Rfree = 0.000) for 11208 atoms. Found 14 (61 requested) and removed 37 (30 requested) atoms. Cycle 34: After refmac, R = 0.1434 (Rfree = 0.000) for 11162 atoms. Found 8 (61 requested) and removed 32 (30 requested) atoms. Cycle 35: After refmac, R = 0.1427 (Rfree = 0.000) for 11126 atoms. Found 10 (61 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 11311 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11329 seeds are put forward Round 1: 528 peptides, 114 chains. Longest chain 10 peptides. Score 0.246 Round 2: 610 peptides, 114 chains. Longest chain 14 peptides. Score 0.329 Round 3: 608 peptides, 110 chains. Longest chain 13 peptides. Score 0.344 Round 4: 594 peptides, 109 chains. Longest chain 13 peptides. Score 0.335 Round 5: 587 peptides, 103 chains. Longest chain 16 peptides. Score 0.353 Taking the results from Round 5 Chains 103, Residues 484, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 17103 reflections ( 95.07 % complete ) and 26625 restraints for refining 11287 atoms. 24765 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1878 (Rfree = 0.000) for 11287 atoms. Found 34 (62 requested) and removed 44 (31 requested) atoms. Cycle 37: After refmac, R = 0.1891 (Rfree = 0.000) for 11226 atoms. Found 38 (62 requested) and removed 45 (31 requested) atoms. Cycle 38: After refmac, R = 0.1881 (Rfree = 0.000) for 11193 atoms. Found 54 (61 requested) and removed 41 (30 requested) atoms. Cycle 39: After refmac, R = 0.1457 (Rfree = 0.000) for 11179 atoms. Found 8 (61 requested) and removed 31 (30 requested) atoms. Cycle 40: After refmac, R = 0.1370 (Rfree = 0.000) for 11139 atoms. Found 2 (61 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 11301 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 11318 seeds are put forward Round 1: 496 peptides, 108 chains. Longest chain 10 peptides. Score 0.239 Round 2: 600 peptides, 113 chains. Longest chain 11 peptides. Score 0.324 Round 3: 620 peptides, 113 chains. Longest chain 12 peptides. Score 0.343 Round 4: 601 peptides, 107 chains. Longest chain 14 peptides. Score 0.350 Round 5: 607 peptides, 104 chains. Longest chain 17 peptides. Score 0.368 Taking the results from Round 5 Chains 104, Residues 503, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26372 restraints for refining 11288 atoms. 24443 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1896 (Rfree = 0.000) for 11288 atoms. Found 34 (62 requested) and removed 42 (31 requested) atoms. Cycle 42: After refmac, R = 0.1960 (Rfree = 0.000) for 11242 atoms. Found 51 (62 requested) and removed 53 (31 requested) atoms. Cycle 43: After refmac, R = 0.1827 (Rfree = 0.000) for 11210 atoms. Found 40 (61 requested) and removed 41 (30 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1905 (Rfree = 0.000) for 11187 atoms. Found 54 (61 requested) and removed 44 (30 requested) atoms. Cycle 45: After refmac, R = 0.1807 (Rfree = 0.000) for 11173 atoms. Found 50 (61 requested) and removed 41 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 11351 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11368 seeds are put forward Round 1: 460 peptides, 101 chains. Longest chain 12 peptides. Score 0.231 Round 2: 533 peptides, 103 chains. Longest chain 15 peptides. Score 0.300 Round 3: 524 peptides, 98 chains. Longest chain 11 peptides. Score 0.312 Round 4: 549 peptides, 102 chains. Longest chain 12 peptides. Score 0.320 Round 5: 536 peptides, 99 chains. Longest chain 13 peptides. Score 0.320 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 99, Residues 437, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2awa-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17103 reflections ( 95.07 % complete ) and 26619 restraints for refining 11288 atoms. 24932 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1879 (Rfree = 0.000) for 11288 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.1944 (Rfree = 0.000) for 11210 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.1875 (Rfree = 0.000) for 11149 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1535 (Rfree = 0.000) for 11092 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Writing output files ... TimeTaking 101.68