Mon 24 Dec 01:04:46 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.4-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 01:04:51 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.4-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 1201 and 0 Target number of residues in the AU: 1201 Target solvent content: 0.6414 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-3.4-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-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.80 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 3.400 Wilson plot Bfac: 72.77 23980 reflections ( 95.89 % complete ) and 0 restraints for refining 13927 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3563 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 13927 atoms. Found 86 (105 requested) and removed 108 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 14067 seeds are put forward NCS extension: 0 residues added, 14067 seeds are put forward Round 1: 533 peptides, 108 chains. Longest chain 11 peptides. Score 0.278 Round 2: 707 peptides, 124 chains. Longest chain 14 peptides. Score 0.380 Round 3: 778 peptides, 138 chains. Longest chain 19 peptides. Score 0.390 Round 4: 787 peptides, 130 chains. Longest chain 21 peptides. Score 0.428 Round 5: 814 peptides, 127 chains. Longest chain 30 peptides. Score 0.461 Taking the results from Round 5 Chains 127, Residues 687, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25960 restraints for refining 11345 atoms. 23339 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2464 (Rfree = 0.000) for 11345 atoms. Found 58 (85 requested) and removed 69 (42 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2273 (Rfree = 0.000) for 11215 atoms. Found 20 (85 requested) and removed 54 (42 requested) atoms. Cycle 3: After refmac, R = 0.2269 (Rfree = 0.000) for 11131 atoms. Found 15 (84 requested) and removed 52 (42 requested) atoms. Cycle 4: After refmac, R = 0.2260 (Rfree = 0.000) for 11059 atoms. Found 22 (83 requested) and removed 48 (41 requested) atoms. Cycle 5: After refmac, R = 0.2209 (Rfree = 0.000) for 11011 atoms. Found 12 (83 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 11275 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 11296 seeds are put forward Round 1: 724 peptides, 135 chains. Longest chain 20 peptides. Score 0.352 Round 2: 824 peptides, 130 chains. Longest chain 23 peptides. Score 0.459 Round 3: 819 peptides, 125 chains. Longest chain 21 peptides. Score 0.472 Round 4: 851 peptides, 133 chains. Longest chain 22 peptides. Score 0.470 Round 5: 852 peptides, 132 chains. Longest chain 21 peptides. Score 0.474 Taking the results from Round 5 Chains 132, Residues 720, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25678 restraints for refining 11348 atoms. 22914 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2320 (Rfree = 0.000) for 11348 atoms. Found 39 (85 requested) and removed 63 (42 requested) atoms. Cycle 7: After refmac, R = 0.2128 (Rfree = 0.000) for 11247 atoms. Found 12 (85 requested) and removed 50 (42 requested) atoms. Cycle 8: After refmac, R = 0.2115 (Rfree = 0.000) for 11176 atoms. Found 12 (84 requested) and removed 49 (42 requested) atoms. Cycle 9: After refmac, R = 0.2140 (Rfree = 0.000) for 11126 atoms. Found 18 (84 requested) and removed 47 (42 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2091 (Rfree = 0.000) for 11078 atoms. Found 10 (83 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 11316 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 11336 seeds are put forward Round 1: 773 peptides, 142 chains. Longest chain 19 peptides. Score 0.370 Round 2: 817 peptides, 131 chains. Longest chain 19 peptides. Score 0.449 Round 3: 854 peptides, 134 chains. Longest chain 22 peptides. Score 0.469 Round 4: 843 peptides, 129 chains. Longest chain 20 peptides. Score 0.478 Round 5: 840 peptides, 124 chains. Longest chain 27 peptides. Score 0.493 Taking the results from Round 5 Chains 127, Residues 716, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25423 restraints for refining 11345 atoms. 22594 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2309 (Rfree = 0.000) for 11345 atoms. Found 44 (85 requested) and removed 61 (42 requested) atoms. Cycle 12: After refmac, R = 0.2128 (Rfree = 0.000) for 11268 atoms. Found 13 (85 requested) and removed 46 (42 requested) atoms. Cycle 13: After refmac, R = 0.2075 (Rfree = 0.000) for 11215 atoms. Found 17 (84 requested) and removed 45 (42 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2061 (Rfree = 0.000) for 11163 atoms. Found 16 (84 requested) and removed 51 (42 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 11113 atoms. Found 13 (84 requested) and removed 47 (42 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11313 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11328 seeds are put forward Round 1: 694 peptides, 130 chains. Longest chain 12 peptides. Score 0.344 Round 2: 799 peptides, 125 chains. Longest chain 20 peptides. Score 0.456 Round 3: 790 peptides, 120 chains. Longest chain 16 peptides. Score 0.467 Round 4: 827 peptides, 124 chains. Longest chain 18 peptides. Score 0.482 Round 5: 806 peptides, 122 chains. Longest chain 17 peptides. Score 0.473 Taking the results from Round 4 Chains 125, Residues 703, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25663 restraints for refining 11347 atoms. 22894 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2237 (Rfree = 0.000) for 11347 atoms. Found 44 (85 requested) and removed 48 (42 requested) atoms. Cycle 17: After refmac, R = 0.2163 (Rfree = 0.000) for 11309 atoms. Found 31 (85 requested) and removed 51 (42 requested) atoms. Cycle 18: After refmac, R = 0.2115 (Rfree = 0.000) for 11263 atoms. Found 22 (85 requested) and removed 45 (42 requested) atoms. Cycle 19: After refmac, R = 0.2037 (Rfree = 0.000) for 11219 atoms. Found 20 (84 requested) and removed 48 (42 requested) atoms. Cycle 20: After refmac, R = 0.2019 (Rfree = 0.000) for 11167 atoms. Found 26 (84 requested) and removed 47 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 11412 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 11432 seeds are put forward Round 1: 686 peptides, 129 chains. Longest chain 14 peptides. Score 0.341 Round 2: 786 peptides, 124 chains. Longest chain 16 peptides. Score 0.449 Round 3: 796 peptides, 121 chains. Longest chain 17 peptides. Score 0.468 Round 4: 793 peptides, 116 chains. Longest chain 22 peptides. Score 0.484 Round 5: 804 peptides, 115 chains. Longest chain 15 peptides. Score 0.496 Taking the results from Round 5 Chains 115, Residues 689, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25647 restraints for refining 11347 atoms. 23006 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2107 (Rfree = 0.000) for 11347 atoms. Found 51 (85 requested) and removed 48 (42 requested) atoms. Cycle 22: After refmac, R = 0.1995 (Rfree = 0.000) for 11305 atoms. Found 23 (85 requested) and removed 47 (42 requested) atoms. Cycle 23: After refmac, R = 0.1969 (Rfree = 0.000) for 11258 atoms. Found 20 (85 requested) and removed 48 (42 requested) atoms. Cycle 24: After refmac, R = 0.1928 (Rfree = 0.000) for 11219 atoms. Found 27 (84 requested) and removed 46 (42 requested) atoms. Cycle 25: After refmac, R = 0.1915 (Rfree = 0.000) for 11185 atoms. Found 18 (84 requested) and removed 45 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11427 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11443 seeds are put forward Round 1: 674 peptides, 126 chains. Longest chain 12 peptides. Score 0.341 Round 2: 784 peptides, 126 chains. Longest chain 15 peptides. Score 0.440 Round 3: 768 peptides, 117 chains. Longest chain 15 peptides. Score 0.460 Round 4: 789 peptides, 117 chains. Longest chain 18 peptides. Score 0.477 Round 5: 772 peptides, 116 chains. Longest chain 20 peptides. Score 0.466 Taking the results from Round 4 Chains 117, Residues 672, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25609 restraints for refining 11347 atoms. 23017 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2050 (Rfree = 0.000) for 11347 atoms. Found 42 (85 requested) and removed 47 (42 requested) atoms. Cycle 27: After refmac, R = 0.1986 (Rfree = 0.000) for 11302 atoms. Found 21 (85 requested) and removed 46 (42 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1934 (Rfree = 0.000) for 11263 atoms. Found 12 (85 requested) and removed 44 (42 requested) atoms. Cycle 29: After refmac, R = 0.1900 (Rfree = 0.000) for 11211 atoms. Found 17 (84 requested) and removed 46 (42 requested) atoms. Cycle 30: After refmac, R = 0.1873 (Rfree = 0.000) for 11172 atoms. Found 29 (84 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11370 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11388 seeds are put forward Round 1: 674 peptides, 133 chains. Longest chain 13 peptides. Score 0.313 Round 2: 736 peptides, 118 chains. Longest chain 18 peptides. Score 0.429 Round 3: 748 peptides, 117 chains. Longest chain 21 peptides. Score 0.443 Round 4: 719 peptides, 111 chains. Longest chain 18 peptides. Score 0.440 Round 5: 735 peptides, 111 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 5 Chains 112, Residues 624, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25868 restraints for refining 11346 atoms. 23426 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2010 (Rfree = 0.000) for 11346 atoms. Found 39 (85 requested) and removed 43 (42 requested) atoms. Cycle 32: After refmac, R = 0.1965 (Rfree = 0.000) for 11316 atoms. Found 28 (85 requested) and removed 48 (42 requested) atoms. Cycle 33: After refmac, R = 0.1885 (Rfree = 0.000) for 11268 atoms. Found 26 (85 requested) and removed 46 (42 requested) atoms. Cycle 34: After refmac, R = 0.1832 (Rfree = 0.000) for 11232 atoms. Found 13 (84 requested) and removed 44 (42 requested) atoms. Cycle 35: After refmac, R = 0.1811 (Rfree = 0.000) for 11197 atoms. Found 20 (84 requested) and removed 46 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11408 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11426 seeds are put forward Round 1: 628 peptides, 123 chains. Longest chain 10 peptides. Score 0.309 Round 2: 682 peptides, 110 chains. Longest chain 17 peptides. Score 0.412 Round 3: 705 peptides, 115 chains. Longest chain 20 peptides. Score 0.413 Round 4: 725 peptides, 113 chains. Longest chain 18 peptides. Score 0.438 Round 5: 735 peptides, 120 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 4 Chains 113, Residues 612, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25934 restraints for refining 11348 atoms. 23599 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1952 (Rfree = 0.000) for 11348 atoms. Found 44 (85 requested) and removed 45 (42 requested) atoms. Cycle 37: After refmac, R = 0.1882 (Rfree = 0.000) for 11319 atoms. Found 16 (85 requested) and removed 42 (42 requested) atoms. Cycle 38: After refmac, R = 0.1839 (Rfree = 0.000) for 11279 atoms. Found 27 (85 requested) and removed 43 (42 requested) atoms. Cycle 39: After refmac, R = 0.1797 (Rfree = 0.000) for 11251 atoms. Found 15 (85 requested) and removed 44 (42 requested) atoms. Cycle 40: After refmac, R = 0.1758 (Rfree = 0.000) for 11209 atoms. Found 17 (84 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11393 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11409 seeds are put forward Round 1: 626 peptides, 126 chains. Longest chain 10 peptides. Score 0.295 Round 2: 698 peptides, 115 chains. Longest chain 18 peptides. Score 0.407 Round 3: 708 peptides, 117 chains. Longest chain 17 peptides. Score 0.408 Round 4: 716 peptides, 115 chains. Longest chain 18 peptides. Score 0.423 Round 5: 717 peptides, 118 chains. Longest chain 18 peptides. Score 0.412 Taking the results from Round 4 Chains 115, Residues 601, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25938 restraints for refining 11348 atoms. 23649 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1867 (Rfree = 0.000) for 11348 atoms. Found 43 (85 requested) and removed 46 (42 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1765 (Rfree = 0.000) for 11319 atoms. Found 20 (85 requested) and removed 43 (42 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1751 (Rfree = 0.000) for 11288 atoms. Found 17 (85 requested) and removed 43 (42 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1742 (Rfree = 0.000) for 11257 atoms. Found 24 (85 requested) and removed 44 (42 requested) atoms. Cycle 45: After refmac, R = 0.1715 (Rfree = 0.000) for 11229 atoms. Found 22 (84 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 11425 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 11454 seeds are put forward Round 1: 591 peptides, 113 chains. Longest chain 12 peptides. Score 0.315 Round 2: 656 peptides, 103 chains. Longest chain 15 peptides. Score 0.416 Round 3: 659 peptides, 113 chains. Longest chain 15 peptides. Score 0.380 Round 4: 663 peptides, 101 chains. Longest chain 18 peptides. Score 0.430 Round 5: 647 peptides, 100 chains. Longest chain 22 peptides. Score 0.420 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 101, Residues 562, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2awa-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23980 reflections ( 95.89 % complete ) and 25906 restraints for refining 11347 atoms. 23715 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1797 (Rfree = 0.000) for 11347 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.1777 (Rfree = 0.000) for 11296 atoms. Found 0 (85 requested) and removed 28 (42 requested) atoms. Cycle 48: After refmac, R = 0.1784 (Rfree = 0.000) for 11253 atoms. Found 0 (85 requested) and removed 39 (42 requested) atoms. Cycle 49: After refmac, R = 0.1753 (Rfree = 0.000) for 11205 atoms. TimeTaking 131.53