Sun 23 Dec 23:42:12 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 2p10-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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/2p10-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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 ============================================================ Sun 23 Dec 23:42:17 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/2p10-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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 1409 and 0 Target number of residues in the AU: 1409 Target solvent content: 0.6714 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: 2p10-4.0-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-4.0-parrot-mrncs.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 4.001 Wilson plot Bfac: 93.52 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 18377 reflections ( 96.69 % complete ) and 0 restraints for refining 15220 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3161 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3076 (Rfree = 0.000) for 15220 atoms. Found 72 (72 requested) and removed 1002 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.35 Search for helices and strands: 0 residues in 0 chains, 14431 seeds are put forward NCS extension: 0 residues added, 14431 seeds are put forward Round 1: 460 peptides, 94 chains. Longest chain 11 peptides. Score 0.249 Round 2: 614 peptides, 107 chains. Longest chain 16 peptides. Score 0.331 Round 3: 717 peptides, 117 chains. Longest chain 22 peptides. Score 0.376 Round 4: 740 peptides, 116 chains. Longest chain 22 peptides. Score 0.396 Round 5: 745 peptides, 121 chains. Longest chain 20 peptides. Score 0.383 Taking the results from Round 4 Chains 122, Residues 624, Estimated correctness of the model 0.0 % 34 chains (180 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28468 restraints for refining 12393 atoms. 25636 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2551 (Rfree = 0.000) for 12393 atoms. Found 58 (58 requested) and removed 296 (29 requested) atoms. Cycle 2: After refmac, R = 0.2277 (Rfree = 0.000) for 11911 atoms. Found 57 (57 requested) and removed 109 (28 requested) atoms. Cycle 3: After refmac, R = 0.2117 (Rfree = 0.000) for 11713 atoms. Found 56 (56 requested) and removed 109 (28 requested) atoms. Cycle 4: After refmac, R = 0.2057 (Rfree = 0.000) for 11590 atoms. Found 55 (55 requested) and removed 61 (27 requested) atoms. Cycle 5: After refmac, R = 0.2004 (Rfree = 0.000) for 11534 atoms. Found 55 (55 requested) and removed 95 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.29 Search for helices and strands: 0 residues in 0 chains, 11959 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 11969 seeds are put forward Round 1: 808 peptides, 137 chains. Longest chain 17 peptides. Score 0.378 Round 2: 884 peptides, 119 chains. Longest chain 22 peptides. Score 0.484 Round 3: 895 peptides, 111 chains. Longest chain 23 peptides. Score 0.514 Round 4: 881 peptides, 101 chains. Longest chain 30 peptides. Score 0.534 Round 5: 918 peptides, 106 chains. Longest chain 26 peptides. Score 0.542 Taking the results from Round 5 Chains 112, Residues 812, Estimated correctness of the model 0.0 % 9 chains (95 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 26996 restraints for refining 12126 atoms. 23586 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2075 (Rfree = 0.000) for 12126 atoms. Found 57 (57 requested) and removed 289 (28 requested) atoms. Cycle 7: After refmac, R = 0.1998 (Rfree = 0.000) for 11728 atoms. Found 56 (56 requested) and removed 181 (28 requested) atoms. Cycle 8: After refmac, R = 0.1901 (Rfree = 0.000) for 11532 atoms. Found 55 (55 requested) and removed 111 (27 requested) atoms. Cycle 9: After refmac, R = 0.1840 (Rfree = 0.000) for 11417 atoms. Found 54 (54 requested) and removed 104 (27 requested) atoms. Cycle 10: After refmac, R = 0.1773 (Rfree = 0.000) for 11317 atoms. Found 53 (53 requested) and removed 82 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.31 Search for helices and strands: 0 residues in 0 chains, 11678 seeds are put forward NCS extension: 46 residues added (2 deleted due to clashes), 11724 seeds are put forward Round 1: 800 peptides, 134 chains. Longest chain 16 peptides. Score 0.382 Round 2: 855 peptides, 120 chains. Longest chain 24 peptides. Score 0.463 Round 3: 850 peptides, 113 chains. Longest chain 24 peptides. Score 0.480 Round 4: 847 peptides, 106 chains. Longest chain 18 peptides. Score 0.499 Round 5: 870 peptides, 107 chains. Longest chain 23 peptides. Score 0.510 Taking the results from Round 5 Chains 116, Residues 763, Estimated correctness of the model 0.0 % 18 chains (123 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 26597 restraints for refining 12082 atoms. 23333 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2075 (Rfree = 0.000) for 12082 atoms. Found 57 (57 requested) and removed 167 (28 requested) atoms. Cycle 12: After refmac, R = 0.1912 (Rfree = 0.000) for 11851 atoms. Found 56 (56 requested) and removed 145 (28 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1850 (Rfree = 0.000) for 11710 atoms. Found 55 (55 requested) and removed 87 (27 requested) atoms. Cycle 14: After refmac, R = 0.1807 (Rfree = 0.000) for 11629 atoms. Found 55 (55 requested) and removed 84 (27 requested) atoms. Cycle 15: After refmac, R = 0.1787 (Rfree = 0.000) for 11566 atoms. Found 55 (55 requested) and removed 88 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 11964 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11982 seeds are put forward Round 1: 793 peptides, 123 chains. Longest chain 18 peptides. Score 0.411 Round 2: 850 peptides, 115 chains. Longest chain 21 peptides. Score 0.474 Round 3: 843 peptides, 108 chains. Longest chain 25 peptides. Score 0.490 Round 4: 856 peptides, 106 chains. Longest chain 30 peptides. Score 0.504 Round 5: 879 peptides, 107 chains. Longest chain 30 peptides. Score 0.516 Taking the results from Round 5 Chains 118, Residues 772, Estimated correctness of the model 0.0 % 17 chains (134 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27589 restraints for refining 12397 atoms. 24236 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2061 (Rfree = 0.000) for 12397 atoms. Found 58 (58 requested) and removed 214 (29 requested) atoms. Cycle 17: After refmac, R = 0.1960 (Rfree = 0.000) for 12117 atoms. Found 58 (58 requested) and removed 109 (29 requested) atoms. Cycle 18: After refmac, R = 0.1918 (Rfree = 0.000) for 11998 atoms. Found 57 (57 requested) and removed 82 (28 requested) atoms. Cycle 19: After refmac, R = 0.1958 (Rfree = 0.000) for 11908 atoms. Found 56 (56 requested) and removed 93 (28 requested) atoms. Cycle 20: After refmac, R = 0.1847 (Rfree = 0.000) for 11832 atoms. Found 56 (56 requested) and removed 82 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.36 Search for helices and strands: 0 residues in 0 chains, 12204 seeds are put forward NCS extension: 34 residues added (11 deleted due to clashes), 12238 seeds are put forward Round 1: 759 peptides, 140 chains. Longest chain 14 peptides. Score 0.332 Round 2: 837 peptides, 113 chains. Longest chain 23 peptides. Score 0.472 Round 3: 830 peptides, 121 chains. Longest chain 24 peptides. Score 0.443 Round 4: 841 peptides, 106 chains. Longest chain 23 peptides. Score 0.495 Round 5: 843 peptides, 115 chains. Longest chain 24 peptides. Score 0.470 Taking the results from Round 4 Chains 114, Residues 735, Estimated correctness of the model 0.0 % 19 chains (164 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27391 restraints for refining 12394 atoms. 24067 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2087 (Rfree = 0.000) for 12394 atoms. Found 58 (58 requested) and removed 165 (29 requested) atoms. Cycle 22: After refmac, R = 0.1965 (Rfree = 0.000) for 12151 atoms. Found 58 (58 requested) and removed 107 (29 requested) atoms. Cycle 23: After refmac, R = 0.1890 (Rfree = 0.000) for 12036 atoms. Found 57 (57 requested) and removed 104 (28 requested) atoms. Cycle 24: After refmac, R = 0.1845 (Rfree = 0.000) for 11938 atoms. Found 56 (56 requested) and removed 87 (28 requested) atoms. Cycle 25: After refmac, R = 0.1536 (Rfree = 0.000) for 11862 atoms. Found 14 (56 requested) and removed 55 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 12190 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 12208 seeds are put forward Round 1: 715 peptides, 129 chains. Longest chain 11 peptides. Score 0.335 Round 2: 818 peptides, 118 chains. Longest chain 21 peptides. Score 0.444 Round 3: 827 peptides, 113 chains. Longest chain 33 peptides. Score 0.465 Round 4: 811 peptides, 113 chains. Longest chain 33 peptides. Score 0.454 Round 5: 818 peptides, 115 chains. Longest chain 19 peptides. Score 0.453 Taking the results from Round 3 Chains 119, Residues 714, Estimated correctness of the model 0.0 % 12 chains (99 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27738 restraints for refining 12316 atoms. 24743 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2068 (Rfree = 0.000) for 12316 atoms. Found 58 (58 requested) and removed 146 (29 requested) atoms. Cycle 27: After refmac, R = 0.1943 (Rfree = 0.000) for 12149 atoms. Found 58 (58 requested) and removed 111 (29 requested) atoms. Cycle 28: After refmac, R = 0.1839 (Rfree = 0.000) for 12030 atoms. Found 57 (57 requested) and removed 71 (28 requested) atoms. Cycle 29: After refmac, R = 0.1826 (Rfree = 0.000) for 11971 atoms. Found 57 (57 requested) and removed 74 (28 requested) atoms. Cycle 30: After refmac, R = 0.1782 (Rfree = 0.000) for 11920 atoms. Found 56 (56 requested) and removed 76 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.32 Search for helices and strands: 0 residues in 0 chains, 12333 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12352 seeds are put forward Round 1: 720 peptides, 133 chains. Longest chain 12 peptides. Score 0.325 Round 2: 826 peptides, 126 chains. Longest chain 28 peptides. Score 0.425 Round 3: 829 peptides, 121 chains. Longest chain 28 peptides. Score 0.442 Round 4: 848 peptides, 120 chains. Longest chain 16 peptides. Score 0.458 Round 5: 853 peptides, 112 chains. Longest chain 28 peptides. Score 0.485 Taking the results from Round 5 Chains 117, Residues 741, Estimated correctness of the model 0.0 % 17 chains (115 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 18377 reflections ( 96.69 % complete ) and 27216 restraints for refining 12395 atoms. 24026 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1917 (Rfree = 0.000) for 12395 atoms. Found 58 (58 requested) and removed 134 (29 requested) atoms. Cycle 32: After refmac, R = 0.1860 (Rfree = 0.000) for 12211 atoms. Found 58 (58 requested) and removed 103 (29 requested) atoms. Cycle 33: After refmac, R = 0.1792 (Rfree = 0.000) for 12107 atoms. Found 57 (57 requested) and removed 88 (28 requested) atoms. Cycle 34: After refmac, R = 0.1765 (Rfree = 0.000) for 12032 atoms. Found 57 (57 requested) and removed 73 (28 requested) atoms. Cycle 35: After refmac, R = 0.1746 (Rfree = 0.000) for 11984 atoms. Found 57 (57 requested) and removed 70 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 12393 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 12412 seeds are put forward Round 1: 688 peptides, 125 chains. Longest chain 17 peptides. Score 0.327 Round 2: 756 peptides, 110 chains. Longest chain 25 peptides. Score 0.426 Round 3: 768 peptides, 115 chains. Longest chain 17 peptides. Score 0.419 Round 4: 775 peptides, 107 chains. Longest chain 30 peptides. Score 0.449 Round 5: 763 peptides, 109 chains. Longest chain 17 peptides. Score 0.434 Taking the results from Round 4 Chains 110, Residues 668, Estimated correctness of the model 0.0 % 18 chains (119 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28057 restraints for refining 12394 atoms. 25178 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1953 (Rfree = 0.000) for 12394 atoms. Found 58 (58 requested) and removed 114 (29 requested) atoms. Cycle 37: After refmac, R = 0.1898 (Rfree = 0.000) for 12265 atoms. Found 58 (58 requested) and removed 91 (29 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1878 (Rfree = 0.000) for 12191 atoms. Found 58 (58 requested) and removed 72 (29 requested) atoms. Cycle 39: After refmac, R = 0.1822 (Rfree = 0.000) for 12126 atoms. Found 57 (57 requested) and removed 75 (28 requested) atoms. Cycle 40: After refmac, R = 0.1840 (Rfree = 0.000) for 12069 atoms. Found 57 (57 requested) and removed 69 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 12451 seeds are put forward NCS extension: 46 residues added (0 deleted due to clashes), 12497 seeds are put forward Round 1: 646 peptides, 126 chains. Longest chain 13 peptides. Score 0.290 Round 2: 733 peptides, 120 chains. Longest chain 24 peptides. Score 0.378 Round 3: 737 peptides, 121 chains. Longest chain 15 peptides. Score 0.377 Round 4: 765 peptides, 120 chains. Longest chain 16 peptides. Score 0.401 Round 5: 748 peptides, 113 chains. Longest chain 21 peptides. Score 0.411 Taking the results from Round 5 Chains 113, Residues 635, Estimated correctness of the model 0.0 % 11 chains (58 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28521 restraints for refining 12396 atoms. 25939 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1921 (Rfree = 0.000) for 12396 atoms. Found 58 (58 requested) and removed 102 (29 requested) atoms. Cycle 42: After refmac, R = 0.1991 (Rfree = 0.000) for 12250 atoms. Found 58 (58 requested) and removed 74 (29 requested) atoms. Cycle 43: After refmac, R = 0.1956 (Rfree = 0.000) for 12165 atoms. Found 58 (58 requested) and removed 71 (29 requested) atoms. Cycle 44: After refmac, R = 0.1851 (Rfree = 0.000) for 12097 atoms. Found 57 (57 requested) and removed 53 (28 requested) atoms. Cycle 45: After refmac, R = 0.1464 (Rfree = 0.000) for 12077 atoms. Found 16 (57 requested) and removed 48 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.30 Search for helices and strands: 0 residues in 0 chains, 12457 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 12484 seeds are put forward Round 1: 565 peptides, 119 chains. Longest chain 12 peptides. Score 0.248 Round 2: 661 peptides, 118 chains. Longest chain 14 peptides. Score 0.330 Round 3: 694 peptides, 117 chains. Longest chain 15 peptides. Score 0.359 Round 4: 706 peptides, 111 chains. Longest chain 16 peptides. Score 0.387 Round 5: 700 peptides, 108 chains. Longest chain 20 peptides. Score 0.393 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 109, Residues 592, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2p10-4_warpNtrace.pdb as input Building loops using Loopy2018 109 chains (592 residues) following loop building 5 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18377 reflections ( 96.69 % complete ) and 28988 restraints for refining 12349 atoms. 26609 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1906 (Rfree = 0.000) for 12349 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.1873 (Rfree = 0.000) for 12250 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.1894 (Rfree = 0.000) for 12170 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.1792 (Rfree = 0.000) for 12109 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Writing output files ... TimeTaking 163