null Mon 24 Dec 07:32:49 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 2p10-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-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/2p10-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-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 07:32:54 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/2p10-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-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 1464 and 0 Target number of residues in the AU: 1464 Target solvent content: 0.6585 Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-3.8-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.90 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: 119.449 3.800 Wilson plot Bfac: 83.94 21461 reflections ( 96.88 % complete ) and 0 restraints for refining 15197 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3132 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2818 (Rfree = 0.000) for 15197 atoms. Found 83 (83 requested) and removed 162 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 15448 seeds are put forward NCS extension: 0 residues added, 15448 seeds are put forward Round 1: 758 peptides, 136 chains. Longest chain 14 peptides. Score 0.344 Round 2: 922 peptides, 127 chains. Longest chain 17 peptides. Score 0.485 Round 3: 963 peptides, 115 chains. Longest chain 29 peptides. Score 0.544 Round 4: 949 peptides, 102 chains. Longest chain 32 peptides. Score 0.570 Round 5: 979 peptides, 103 chains. Longest chain 31 peptides. Score 0.584 Taking the results from Round 5 Chains 119, Residues 876, Estimated correctness of the model 0.0 % 24 chains (245 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26031 restraints for refining 12412 atoms. 21917 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2303 (Rfree = 0.000) for 12412 atoms. Found 68 (68 requested) and removed 117 (34 requested) atoms. Cycle 2: After refmac, R = 0.2167 (Rfree = 0.000) for 12100 atoms. Found 59 (67 requested) and removed 78 (33 requested) atoms. Cycle 3: After refmac, R = 0.2115 (Rfree = 0.000) for 11980 atoms. Found 40 (66 requested) and removed 53 (33 requested) atoms. Cycle 4: After refmac, R = 0.2057 (Rfree = 0.000) for 11894 atoms. Found 41 (65 requested) and removed 47 (32 requested) atoms. Cycle 5: After refmac, R = 0.1992 (Rfree = 0.000) for 11835 atoms. Found 40 (65 requested) and removed 47 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 12296 seeds are put forward NCS extension: 8 residues added (6 deleted due to clashes), 12304 seeds are put forward Round 1: 899 peptides, 137 chains. Longest chain 36 peptides. Score 0.441 Round 2: 961 peptides, 114 chains. Longest chain 33 peptides. Score 0.545 Round 3: 975 peptides, 115 chains. Longest chain 36 peptides. Score 0.551 Round 4: 978 peptides, 101 chains. Longest chain 33 peptides. Score 0.589 Round 5: 993 peptides, 103 chains. Longest chain 36 peptides. Score 0.592 Taking the results from Round 5 Chains 116, Residues 890, Estimated correctness of the model 0.0 % 19 chains (197 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26136 restraints for refining 12376 atoms. 22056 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2274 (Rfree = 0.000) for 12376 atoms. Found 68 (68 requested) and removed 104 (34 requested) atoms. Cycle 7: After refmac, R = 0.2072 (Rfree = 0.000) for 12202 atoms. Found 58 (67 requested) and removed 87 (33 requested) atoms. Cycle 8: After refmac, R = 0.1983 (Rfree = 0.000) for 12103 atoms. Found 28 (66 requested) and removed 56 (33 requested) atoms. Cycle 9: After refmac, R = 0.1921 (Rfree = 0.000) for 12018 atoms. Found 32 (66 requested) and removed 55 (33 requested) atoms. Cycle 10: After refmac, R = 0.1874 (Rfree = 0.000) for 11965 atoms. Found 20 (65 requested) and removed 48 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.18 Search for helices and strands: 0 residues in 0 chains, 12415 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 12436 seeds are put forward Round 1: 924 peptides, 134 chains. Longest chain 27 peptides. Score 0.467 Round 2: 973 peptides, 111 chains. Longest chain 47 peptides. Score 0.560 Round 3: 990 peptides, 115 chains. Longest chain 28 peptides. Score 0.559 Round 4: 978 peptides, 110 chains. Longest chain 39 peptides. Score 0.566 Round 5: 978 peptides, 108 chains. Longest chain 33 peptides. Score 0.571 Taking the results from Round 5 Chains 117, Residues 870, Estimated correctness of the model 0.0 % 14 chains (149 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26967 restraints for refining 12413 atoms. 23128 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2034 (Rfree = 0.000) for 12413 atoms. Found 48 (68 requested) and removed 72 (34 requested) atoms. Cycle 12: After refmac, R = 0.1883 (Rfree = 0.000) for 12265 atoms. Found 25 (68 requested) and removed 68 (34 requested) atoms. Cycle 13: After refmac, R = 0.1842 (Rfree = 0.000) for 12163 atoms. Found 34 (67 requested) and removed 68 (33 requested) atoms. Cycle 14: After refmac, R = 0.1759 (Rfree = 0.000) for 12092 atoms. Found 21 (66 requested) and removed 56 (33 requested) atoms. Cycle 15: After refmac, R = 0.1722 (Rfree = 0.000) for 12017 atoms. Found 19 (66 requested) and removed 42 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.16 Search for helices and strands: 0 residues in 0 chains, 12496 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 12526 seeds are put forward Round 1: 884 peptides, 129 chains. Longest chain 24 peptides. Score 0.455 Round 2: 918 peptides, 118 chains. Longest chain 23 peptides. Score 0.509 Round 3: 946 peptides, 112 chains. Longest chain 34 peptides. Score 0.542 Round 4: 954 peptides, 118 chains. Longest chain 25 peptides. Score 0.530 Round 5: 972 peptides, 110 chains. Longest chain 26 peptides. Score 0.562 Taking the results from Round 5 Chains 121, Residues 862, Estimated correctness of the model 0.0 % 15 chains (135 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27017 restraints for refining 12416 atoms. 23244 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2039 (Rfree = 0.000) for 12416 atoms. Found 59 (68 requested) and removed 62 (34 requested) atoms. Cycle 17: After refmac, R = 0.1864 (Rfree = 0.000) for 12333 atoms. Found 27 (68 requested) and removed 54 (34 requested) atoms. Cycle 18: After refmac, R = 0.1819 (Rfree = 0.000) for 12275 atoms. Found 15 (67 requested) and removed 57 (33 requested) atoms. Cycle 19: After refmac, R = 0.1773 (Rfree = 0.000) for 12205 atoms. Found 18 (67 requested) and removed 54 (33 requested) atoms. Cycle 20: After refmac, R = 0.1782 (Rfree = 0.000) for 12149 atoms. Found 28 (66 requested) and removed 50 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.15 Search for helices and strands: 0 residues in 0 chains, 12610 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 12626 seeds are put forward Round 1: 832 peptides, 133 chains. Longest chain 16 peptides. Score 0.408 Round 2: 920 peptides, 119 chains. Longest chain 33 peptides. Score 0.507 Round 3: 911 peptides, 112 chains. Longest chain 36 peptides. Score 0.521 Round 4: 934 peptides, 109 chains. Longest chain 38 peptides. Score 0.543 Round 5: 899 peptides, 110 chains. Longest chain 34 peptides. Score 0.519 Taking the results from Round 4 Chains 125, Residues 825, Estimated correctness of the model 0.0 % 18 chains (191 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26802 restraints for refining 12411 atoms. 23050 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1997 (Rfree = 0.000) for 12411 atoms. Found 49 (68 requested) and removed 80 (34 requested) atoms. Cycle 22: After refmac, R = 0.1817 (Rfree = 0.000) for 12276 atoms. Found 22 (68 requested) and removed 56 (34 requested) atoms. Cycle 23: After refmac, R = 0.1787 (Rfree = 0.000) for 12183 atoms. Found 17 (67 requested) and removed 48 (33 requested) atoms. Cycle 24: After refmac, R = 0.1813 (Rfree = 0.000) for 12116 atoms. Found 32 (66 requested) and removed 48 (33 requested) atoms. Cycle 25: After refmac, R = 0.1765 (Rfree = 0.000) for 12056 atoms. Found 28 (66 requested) and removed 50 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.15 Search for helices and strands: 0 residues in 0 chains, 12465 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 12483 seeds are put forward Round 1: 833 peptides, 138 chains. Longest chain 24 peptides. Score 0.393 Round 2: 876 peptides, 116 chains. Longest chain 27 peptides. Score 0.488 Round 3: 911 peptides, 114 chains. Longest chain 34 peptides. Score 0.515 Round 4: 918 peptides, 117 chains. Longest chain 29 peptides. Score 0.511 Round 5: 926 peptides, 114 chains. Longest chain 34 peptides. Score 0.525 Taking the results from Round 5 Chains 119, Residues 812, Estimated correctness of the model 0.0 % 9 chains (64 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28266 restraints for refining 12416 atoms. 24943 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1918 (Rfree = 0.000) for 12416 atoms. Found 67 (68 requested) and removed 76 (34 requested) atoms. Cycle 27: After refmac, R = 0.1778 (Rfree = 0.000) for 12339 atoms. Found 20 (68 requested) and removed 50 (34 requested) atoms. Cycle 28: After refmac, R = 0.1745 (Rfree = 0.000) for 12262 atoms. Found 27 (67 requested) and removed 62 (33 requested) atoms. Cycle 29: After refmac, R = 0.1720 (Rfree = 0.000) for 12197 atoms. Found 39 (67 requested) and removed 60 (33 requested) atoms. Cycle 30: After refmac, R = 0.1666 (Rfree = 0.000) for 12144 atoms. Found 32 (66 requested) and removed 50 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.15 Search for helices and strands: 0 residues in 0 chains, 12552 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 12593 seeds are put forward Round 1: 775 peptides, 128 chains. Longest chain 26 peptides. Score 0.383 Round 2: 898 peptides, 126 chains. Longest chain 28 peptides. Score 0.473 Round 3: 891 peptides, 123 chains. Longest chain 24 peptides. Score 0.477 Round 4: 900 peptides, 124 chains. Longest chain 30 peptides. Score 0.480 Round 5: 890 peptides, 112 chains. Longest chain 28 peptides. Score 0.508 Taking the results from Round 5 Chains 127, Residues 778, Estimated correctness of the model 0.0 % 20 chains (189 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26978 restraints for refining 12416 atoms. 23401 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1912 (Rfree = 0.000) for 12416 atoms. Found 46 (68 requested) and removed 69 (34 requested) atoms. Cycle 32: After refmac, R = 0.1797 (Rfree = 0.000) for 12314 atoms. Found 34 (68 requested) and removed 57 (34 requested) atoms. Cycle 33: After refmac, R = 0.1803 (Rfree = 0.000) for 12257 atoms. Found 62 (67 requested) and removed 56 (33 requested) atoms. Cycle 34: After refmac, R = 0.1694 (Rfree = 0.000) for 12240 atoms. Found 30 (67 requested) and removed 44 (33 requested) atoms. Cycle 35: After refmac, R = 0.1668 (Rfree = 0.000) for 12186 atoms. Found 34 (67 requested) and removed 51 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.14 Search for helices and strands: 0 residues in 0 chains, 12618 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 12640 seeds are put forward Round 1: 779 peptides, 138 chains. Longest chain 20 peptides. Score 0.353 Round 2: 867 peptides, 131 chains. Longest chain 19 peptides. Score 0.438 Round 3: 850 peptides, 122 chains. Longest chain 22 peptides. Score 0.453 Round 4: 842 peptides, 122 chains. Longest chain 22 peptides. Score 0.448 Round 5: 881 peptides, 123 chains. Longest chain 36 peptides. Score 0.471 Taking the results from Round 5 Chains 130, Residues 758, Estimated correctness of the model 0.0 % 15 chains (108 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28020 restraints for refining 12416 atoms. 24807 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1885 (Rfree = 0.000) for 12416 atoms. Found 59 (68 requested) and removed 80 (34 requested) atoms. Cycle 37: After refmac, R = 0.1823 (Rfree = 0.000) for 12339 atoms. Found 56 (68 requested) and removed 54 (34 requested) atoms. Cycle 38: After refmac, R = 0.1785 (Rfree = 0.000) for 12299 atoms. Found 67 (67 requested) and removed 52 (33 requested) atoms. Cycle 39: After refmac, R = 0.1703 (Rfree = 0.000) for 12282 atoms. Found 49 (67 requested) and removed 52 (33 requested) atoms. Cycle 40: After refmac, R = 0.1680 (Rfree = 0.000) for 12255 atoms. Found 48 (67 requested) and removed 47 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 12657 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 12682 seeds are put forward Round 1: 725 peptides, 135 chains. Longest chain 14 peptides. Score 0.322 Round 2: 804 peptides, 132 chains. Longest chain 21 peptides. Score 0.391 Round 3: 831 peptides, 128 chains. Longest chain 26 peptides. Score 0.422 Round 4: 819 peptides, 127 chains. Longest chain 16 peptides. Score 0.417 Round 5: 802 peptides, 120 chains. Longest chain 21 peptides. Score 0.427 Taking the results from Round 5 Chains 121, Residues 682, Estimated correctness of the model 0.0 % 12 chains (72 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28986 restraints for refining 12417 atoms. 26178 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1846 (Rfree = 0.000) for 12417 atoms. Found 48 (68 requested) and removed 77 (34 requested) atoms. Cycle 42: After refmac, R = 0.1843 (Rfree = 0.000) for 12327 atoms. Found 66 (68 requested) and removed 47 (34 requested) atoms. Cycle 43: After refmac, R = 0.1816 (Rfree = 0.000) for 12313 atoms. Found 67 (67 requested) and removed 64 (33 requested) atoms. Cycle 44: After refmac, R = 0.1767 (Rfree = 0.000) for 12283 atoms. Found 67 (67 requested) and removed 55 (33 requested) atoms. Cycle 45: After refmac, R = 0.1724 (Rfree = 0.000) for 12275 atoms. Found 67 (67 requested) and removed 51 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 12781 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 12798 seeds are put forward Round 1: 647 peptides, 124 chains. Longest chain 15 peptides. Score 0.298 Round 2: 729 peptides, 119 chains. Longest chain 16 peptides. Score 0.378 Round 3: 725 peptides, 117 chains. Longest chain 17 peptides. Score 0.382 Round 4: 735 peptides, 119 chains. Longest chain 14 peptides. Score 0.382 Round 5: 766 peptides, 116 chains. Longest chain 19 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 118, Residues 650, Estimated correctness of the model 0.0 % 16 chains (90 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 118 chains (650 residues) following loop building 16 chains (90 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21461 reflections ( 96.88 % complete ) and 28959 restraints for refining 12414 atoms. 26230 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1869 (Rfree = 0.000) for 12414 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.1846 (Rfree = 0.000) for 12332 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.1767 (Rfree = 0.000) for 12275 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.1758 (Rfree = 0.000) for 12217 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:15:22 GMT 2018 Job finished. TimeTaking 162.54 Used memory is bytes: 13629144