Mon 24 Dec 07:34:35 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i8d-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-parrot-noncs ############### 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 07:34:39 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-parrot-noncs/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 210 and 0 Target number of residues in the AU: 210 Target solvent content: 0.6243 Checking the provided sequence file Detected sequence length: 123 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 246 Adjusted target solvent content: 0.56 Input MTZ file: 2i8d-3.4-parrot-noncs.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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 1968 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: 55.142 3.400 Wilson plot Bfac: 63.50 4439 reflections ( 98.89 % complete ) and 0 restraints for refining 2170 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3377 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2794 (Rfree = 0.000) for 2170 atoms. Found 15 (16 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 0 residues added, 2202 seeds are put forward Round 1: 127 peptides, 21 chains. Longest chain 17 peptides. Score 0.421 Round 2: 153 peptides, 22 chains. Longest chain 14 peptides. Score 0.526 Round 3: 162 peptides, 20 chains. Longest chain 34 peptides. Score 0.601 Round 4: 163 peptides, 19 chains. Longest chain 22 peptides. Score 0.623 Round 5: 152 peptides, 19 chains. Longest chain 29 peptides. Score 0.579 Taking the results from Round 4 Chains 19, Residues 144, Estimated correctness of the model 36.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3752 restraints for refining 1790 atoms. 3195 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2590 (Rfree = 0.000) for 1790 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 2: After refmac, R = 0.2452 (Rfree = 0.000) for 1784 atoms. Found 5 (13 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2405 (Rfree = 0.000) for 1774 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2425 (Rfree = 0.000) for 1771 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2408 (Rfree = 0.000) for 1762 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 1852 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 1882 seeds are put forward Round 1: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.433 Round 2: 151 peptides, 23 chains. Longest chain 13 peptides. Score 0.496 Round 3: 147 peptides, 22 chains. Longest chain 15 peptides. Score 0.498 Round 4: 142 peptides, 18 chains. Longest chain 17 peptides. Score 0.556 Round 5: 141 peptides, 18 chains. Longest chain 20 peptides. Score 0.552 Taking the results from Round 4 Chains 18, Residues 124, Estimated correctness of the model 13.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3927 restraints for refining 1790 atoms. 3449 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2545 (Rfree = 0.000) for 1790 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.2358 (Rfree = 0.000) for 1781 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.2374 (Rfree = 0.000) for 1772 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2381 (Rfree = 0.000) for 1767 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2382 (Rfree = 0.000) for 1763 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1855 seeds are put forward Round 1: 139 peptides, 24 chains. Longest chain 14 peptides. Score 0.416 Round 2: 156 peptides, 23 chains. Longest chain 19 peptides. Score 0.519 Round 3: 158 peptides, 23 chains. Longest chain 12 peptides. Score 0.528 Round 4: 161 peptides, 25 chains. Longest chain 17 peptides. Score 0.502 Round 5: 168 peptides, 24 chains. Longest chain 15 peptides. Score 0.553 Taking the results from Round 5 Chains 24, Residues 144, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3873 restraints for refining 1790 atoms. 3321 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2600 (Rfree = 0.000) for 1790 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.2411 (Rfree = 0.000) for 1784 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2451 (Rfree = 0.000) for 1776 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2403 (Rfree = 0.000) for 1772 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2402 (Rfree = 0.000) for 1768 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1850 seeds are put forward Round 1: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.465 Round 2: 145 peptides, 21 chains. Longest chain 11 peptides. Score 0.509 Round 3: 152 peptides, 20 chains. Longest chain 13 peptides. Score 0.560 Round 4: 164 peptides, 23 chains. Longest chain 14 peptides. Score 0.554 Round 5: 164 peptides, 21 chains. Longest chain 16 peptides. Score 0.591 Taking the results from Round 5 Chains 21, Residues 143, Estimated correctness of the model 25.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3908 restraints for refining 1789 atoms. 3357 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2725 (Rfree = 0.000) for 1789 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.2547 (Rfree = 0.000) for 1788 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2508 (Rfree = 0.000) for 1784 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2508 (Rfree = 0.000) for 1778 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2429 (Rfree = 0.000) for 1773 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1841 seeds are put forward Round 1: 142 peptides, 22 chains. Longest chain 15 peptides. Score 0.474 Round 2: 157 peptides, 18 chains. Longest chain 19 peptides. Score 0.617 Round 3: 157 peptides, 17 chains. Longest chain 20 peptides. Score 0.635 Round 4: 158 peptides, 19 chains. Longest chain 16 peptides. Score 0.603 Round 5: 158 peptides, 18 chains. Longest chain 19 peptides. Score 0.621 Taking the results from Round 3 Chains 17, Residues 140, Estimated correctness of the model 39.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3946 restraints for refining 1790 atoms. 3403 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2630 (Rfree = 0.000) for 1790 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 22: After refmac, R = 0.2544 (Rfree = 0.000) for 1785 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.2464 (Rfree = 0.000) for 1778 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2477 (Rfree = 0.000) for 1774 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2418 (Rfree = 0.000) for 1767 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1846 seeds are put forward Round 1: 137 peptides, 20 chains. Longest chain 12 peptides. Score 0.493 Round 2: 155 peptides, 23 chains. Longest chain 15 peptides. Score 0.515 Round 3: 154 peptides, 21 chains. Longest chain 14 peptides. Score 0.550 Round 4: 156 peptides, 19 chains. Longest chain 16 peptides. Score 0.595 Round 5: 146 peptides, 17 chains. Longest chain 15 peptides. Score 0.592 Taking the results from Round 4 Chains 19, Residues 137, Estimated correctness of the model 27.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3973 restraints for refining 1790 atoms. 3444 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2555 (Rfree = 0.000) for 1790 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2417 (Rfree = 0.000) for 1784 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.2386 (Rfree = 0.000) for 1777 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2306 (Rfree = 0.000) for 1771 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2296 (Rfree = 0.000) for 1764 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 1828 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1844 seeds are put forward Round 1: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.352 Round 2: 147 peptides, 20 chains. Longest chain 13 peptides. Score 0.538 Round 3: 146 peptides, 20 chains. Longest chain 16 peptides. Score 0.534 Round 4: 151 peptides, 20 chains. Longest chain 19 peptides. Score 0.556 Round 5: 153 peptides, 22 chains. Longest chain 15 peptides. Score 0.526 Taking the results from Round 4 Chains 20, Residues 131, Estimated correctness of the model 13.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3964 restraints for refining 1790 atoms. 3460 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2455 (Rfree = 0.000) for 1790 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.2360 (Rfree = 0.000) for 1786 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2357 (Rfree = 0.000) for 1782 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2311 (Rfree = 0.000) for 1780 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2263 (Rfree = 0.000) for 1774 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 1849 seeds are put forward Round 1: 123 peptides, 21 chains. Longest chain 14 peptides. Score 0.400 Round 2: 129 peptides, 20 chains. Longest chain 13 peptides. Score 0.454 Round 3: 129 peptides, 21 chains. Longest chain 12 peptides. Score 0.431 Round 4: 131 peptides, 18 chains. Longest chain 17 peptides. Score 0.506 Round 5: 129 peptides, 16 chains. Longest chain 17 peptides. Score 0.539 Taking the results from Round 5 Chains 16, Residues 113, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 4043 restraints for refining 1790 atoms. 3607 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2553 (Rfree = 0.000) for 1790 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2463 (Rfree = 0.000) for 1788 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2480 (Rfree = 0.000) for 1787 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.2390 (Rfree = 0.000) for 1787 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2387 (Rfree = 0.000) for 1781 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1851 seeds are put forward Round 1: 114 peptides, 17 chains. Longest chain 16 peptides. Score 0.445 Round 2: 131 peptides, 19 chains. Longest chain 17 peptides. Score 0.485 Round 3: 130 peptides, 20 chains. Longest chain 13 peptides. Score 0.459 Round 4: 138 peptides, 17 chains. Longest chain 19 peptides. Score 0.558 Round 5: 131 peptides, 19 chains. Longest chain 15 peptides. Score 0.485 Taking the results from Round 4 Chains 17, Residues 121, Estimated correctness of the model 14.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 4007 restraints for refining 1790 atoms. 3540 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2663 (Rfree = 0.000) for 1790 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.2575 (Rfree = 0.000) for 1793 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2575 (Rfree = 0.000) for 1794 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2521 (Rfree = 0.000) for 1792 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2474 (Rfree = 0.000) for 1789 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward NCS extension: 5 residues added (0 deleted due to clashes), 1844 seeds are put forward Round 1: 105 peptides, 17 chains. Longest chain 13 peptides. Score 0.397 Round 2: 117 peptides, 17 chains. Longest chain 13 peptides. Score 0.460 Round 3: 122 peptides, 16 chains. Longest chain 17 peptides. Score 0.507 Round 4: 120 peptides, 18 chains. Longest chain 13 peptides. Score 0.453 Round 5: 127 peptides, 16 chains. Longest chain 19 peptides. Score 0.530 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 111, Estimated correctness of the model 4.2 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2i8d-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4439 reflections ( 98.89 % complete ) and 3986 restraints for refining 1790 atoms. 3558 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2610 (Rfree = 0.000) for 1790 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2496 (Rfree = 0.000) for 1783 atoms. Found 0 (13 requested) and removed 0 (6 requested) atoms. Cycle 48: After refmac, R = 0.2519 (Rfree = 0.000) for 1782 atoms. Found 0 (13 requested) and removed 0 (6 requested) atoms. Cycle 49: After refmac, R = 0.2384 (Rfree = 0.000) for 1781 atoms. Found 0 (13 requested) and removed 1 (6 requested) atoms. TimeTaking 24.68