Mon 24 Dec 07:50:29 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 2anu-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-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/2anu-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-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 07:50:34 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/2anu-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-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 1351 and 0 Target number of residues in the AU: 1351 Target solvent content: 0.5996 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-3.2-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: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 12240 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: 127.729 3.200 Wilson plot Bfac: 52.43 Failed to save intermediate PDB 29175 reflections ( 99.85 % complete ) and 0 restraints for refining 13525 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2872 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2318 (Rfree = 0.000) for 13525 atoms. Found 121 (121 requested) and removed 88 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 2.82 Search for helices and strands: 0 residues in 0 chains, 13800 seeds are put forward NCS extension: 0 residues added, 13800 seeds are put forward Round 1: 854 peptides, 133 chains. Longest chain 20 peptides. Score 0.471 Round 2: 949 peptides, 115 chains. Longest chain 26 peptides. Score 0.599 Round 3: 1031 peptides, 111 chains. Longest chain 45 peptides. Score 0.661 Round 4: 1063 peptides, 106 chains. Longest chain 41 peptides. Score 0.691 Round 5: 1062 peptides, 97 chains. Longest chain 38 peptides. Score 0.713 Taking the results from Round 5 Chains 109, Residues 965, Estimated correctness of the model 67.9 % 18 chains (343 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 107 A Built loop between residues 134 B and 139 B 105 chains (973 residues) following loop building 16 chains (354 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19981 restraints for refining 11170 atoms. 14646 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2465 (Rfree = 0.000) for 11170 atoms. Found 100 (100 requested) and removed 95 (50 requested) atoms. Cycle 2: After refmac, R = 0.2316 (Rfree = 0.000) for 11053 atoms. Found 69 (98 requested) and removed 63 (50 requested) atoms. Cycle 3: After refmac, R = 0.2190 (Rfree = 0.000) for 10999 atoms. Found 44 (95 requested) and removed 50 (49 requested) atoms. Cycle 4: After refmac, R = 0.2101 (Rfree = 0.000) for 10954 atoms. Found 27 (92 requested) and removed 50 (49 requested) atoms. Cycle 5: After refmac, R = 0.2061 (Rfree = 0.000) for 10905 atoms. Found 29 (90 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.02 2.82 Search for helices and strands: 0 residues in 0 chains, 11200 seeds are put forward NCS extension: 50 residues added (21 deleted due to clashes), 11250 seeds are put forward Round 1: 991 peptides, 111 chains. Longest chain 35 peptides. Score 0.637 Round 2: 1041 peptides, 100 chains. Longest chain 28 peptides. Score 0.695 Round 3: 1050 peptides, 99 chains. Longest chain 38 peptides. Score 0.702 Round 4: 1032 peptides, 95 chains. Longest chain 35 peptides. Score 0.702 Round 5: 1046 peptides, 94 chains. Longest chain 49 peptides. Score 0.712 Taking the results from Round 5 Chains 104, Residues 952, Estimated correctness of the model 67.7 % 17 chains (321 residues) have been docked in sequence Building loops using Loopy2018 104 chains (952 residues) following loop building 17 chains (321 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 21165 restraints for refining 11175 atoms. 16020 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2500 (Rfree = 0.000) for 11175 atoms. Found 90 (90 requested) and removed 86 (50 requested) atoms. Cycle 7: After refmac, R = 0.2294 (Rfree = 0.000) for 11134 atoms. Found 50 (88 requested) and removed 54 (50 requested) atoms. Cycle 8: After refmac, R = 0.2198 (Rfree = 0.000) for 11100 atoms. Found 36 (85 requested) and removed 50 (49 requested) atoms. Cycle 9: After refmac, R = 0.2128 (Rfree = 0.000) for 11070 atoms. Found 29 (83 requested) and removed 49 (49 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2088 (Rfree = 0.000) for 11039 atoms. Found 18 (81 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11296 seeds are put forward NCS extension: 23 residues added (14 deleted due to clashes), 11319 seeds are put forward Round 1: 998 peptides, 107 chains. Longest chain 34 peptides. Score 0.652 Round 2: 1024 peptides, 95 chains. Longest chain 40 peptides. Score 0.698 Round 3: 1043 peptides, 100 chains. Longest chain 37 peptides. Score 0.696 Round 4: 1067 peptides, 95 chains. Longest chain 34 peptides. Score 0.720 Round 5: 1031 peptides, 92 chains. Longest chain 35 peptides. Score 0.709 Taking the results from Round 4 Chains 98, Residues 972, Estimated correctness of the model 69.3 % 14 chains (300 residues) have been docked in sequence Building loops using Loopy2018 98 chains (972 residues) following loop building 14 chains (300 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 20887 restraints for refining 11173 atoms. 15669 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2400 (Rfree = 0.000) for 11173 atoms. Found 80 (80 requested) and removed 80 (50 requested) atoms. Cycle 12: After refmac, R = 0.2200 (Rfree = 0.000) for 11140 atoms. Found 48 (78 requested) and removed 50 (50 requested) atoms. Cycle 13: After refmac, R = 0.2111 (Rfree = 0.000) for 11113 atoms. Found 38 (75 requested) and removed 49 (49 requested) atoms. Cycle 14: After refmac, R = 0.2038 (Rfree = 0.000) for 11086 atoms. Found 19 (73 requested) and removed 49 (49 requested) atoms. Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 11040 atoms. Found 17 (71 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11298 seeds are put forward NCS extension: 27 residues added (18 deleted due to clashes), 11325 seeds are put forward Round 1: 970 peptides, 113 chains. Longest chain 34 peptides. Score 0.618 Round 2: 1036 peptides, 95 chains. Longest chain 39 peptides. Score 0.705 Round 3: 1053 peptides, 90 chains. Longest chain 46 peptides. Score 0.725 Round 4: 1070 peptides, 88 chains. Longest chain 47 peptides. Score 0.738 Round 5: 1074 peptides, 98 chains. Longest chain 40 peptides. Score 0.716 Taking the results from Round 4 Chains 91, Residues 982, Estimated correctness of the model 72.8 % 14 chains (329 residues) have been docked in sequence Building loops using Loopy2018 91 chains (982 residues) following loop building 14 chains (329 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 20724 restraints for refining 11172 atoms. 15358 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2358 (Rfree = 0.000) for 11172 atoms. Found 70 (70 requested) and removed 68 (50 requested) atoms. Cycle 17: After refmac, R = 0.2180 (Rfree = 0.000) for 11130 atoms. Found 47 (68 requested) and removed 52 (50 requested) atoms. Cycle 18: After refmac, R = 0.2067 (Rfree = 0.000) for 11109 atoms. Found 24 (65 requested) and removed 50 (49 requested) atoms. Cycle 19: After refmac, R = 0.2009 (Rfree = 0.000) for 11073 atoms. Found 12 (63 requested) and removed 51 (49 requested) atoms. Cycle 20: After refmac, R = 0.1967 (Rfree = 0.000) for 11024 atoms. Found 15 (61 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11251 seeds are put forward NCS extension: 30 residues added (9 deleted due to clashes), 11281 seeds are put forward Round 1: 974 peptides, 108 chains. Longest chain 28 peptides. Score 0.635 Round 2: 1029 peptides, 96 chains. Longest chain 34 peptides. Score 0.698 Round 3: 1041 peptides, 99 chains. Longest chain 46 peptides. Score 0.697 Round 4: 1010 peptides, 93 chains. Longest chain 35 peptides. Score 0.696 Round 5: 1017 peptides, 96 chains. Longest chain 37 peptides. Score 0.692 Taking the results from Round 2 Chains 100, Residues 933, Estimated correctness of the model 64.8 % 13 chains (245 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 21899 restraints for refining 11174 atoms. 17150 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2212 (Rfree = 0.000) for 11174 atoms. Found 60 (60 requested) and removed 59 (50 requested) atoms. Cycle 22: After refmac, R = 0.2051 (Rfree = 0.000) for 11151 atoms. Found 43 (60 requested) and removed 50 (50 requested) atoms. Cycle 23: After refmac, R = 0.1958 (Rfree = 0.000) for 11131 atoms. Found 25 (60 requested) and removed 50 (50 requested) atoms. Cycle 24: After refmac, R = 0.1924 (Rfree = 0.000) for 11095 atoms. Found 20 (59 requested) and removed 49 (49 requested) atoms. Cycle 25: After refmac, R = 0.1900 (Rfree = 0.000) for 11058 atoms. Found 22 (59 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 11309 seeds are put forward NCS extension: 29 residues added (11 deleted due to clashes), 11338 seeds are put forward Round 1: 947 peptides, 115 chains. Longest chain 27 peptides. Score 0.598 Round 2: 1007 peptides, 103 chains. Longest chain 51 peptides. Score 0.668 Round 3: 1009 peptides, 107 chains. Longest chain 31 peptides. Score 0.659 Round 4: 1024 peptides, 107 chains. Longest chain 37 peptides. Score 0.667 Round 5: 1023 peptides, 111 chains. Longest chain 33 peptides. Score 0.656 Taking the results from Round 2 Chains 106, Residues 904, Estimated correctness of the model 58.1 % 9 chains (200 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 29175 reflections ( 99.85 % complete ) and 22640 restraints for refining 11175 atoms. 18208 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2124 (Rfree = 0.000) for 11175 atoms. Found 60 (60 requested) and removed 66 (50 requested) atoms. Cycle 27: After refmac, R = 0.2005 (Rfree = 0.000) for 11144 atoms. Found 33 (60 requested) and removed 50 (50 requested) atoms. Cycle 28: After refmac, R = 0.1977 (Rfree = 0.000) for 11118 atoms. Found 26 (59 requested) and removed 49 (49 requested) atoms. Cycle 29: After refmac, R = 0.1957 (Rfree = 0.000) for 11083 atoms. Found 34 (59 requested) and removed 52 (49 requested) atoms. Cycle 30: After refmac, R = 0.1947 (Rfree = 0.000) for 11051 atoms. Found 27 (59 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11313 seeds are put forward NCS extension: 34 residues added (41 deleted due to clashes), 11347 seeds are put forward Round 1: 940 peptides, 116 chains. Longest chain 37 peptides. Score 0.590 Round 2: 1005 peptides, 108 chains. Longest chain 45 peptides. Score 0.654 Round 3: 959 peptides, 101 chains. Longest chain 49 peptides. Score 0.646 Round 4: 974 peptides, 104 chains. Longest chain 43 peptides. Score 0.646 Round 5: 996 peptides, 108 chains. Longest chain 44 peptides. Score 0.648 Taking the results from Round 2 Chains 113, Residues 897, Estimated correctness of the model 54.8 % 10 chains (192 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 22900 restraints for refining 11172 atoms. 18548 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2146 (Rfree = 0.000) for 11172 atoms. Found 60 (60 requested) and removed 61 (50 requested) atoms. Cycle 32: After refmac, R = 0.2034 (Rfree = 0.000) for 11145 atoms. Found 41 (60 requested) and removed 52 (50 requested) atoms. Cycle 33: After refmac, R = 0.1998 (Rfree = 0.000) for 11126 atoms. Found 27 (59 requested) and removed 50 (49 requested) atoms. Cycle 34: After refmac, R = 0.1963 (Rfree = 0.000) for 11091 atoms. Found 23 (59 requested) and removed 50 (49 requested) atoms. Cycle 35: After refmac, R = 0.1940 (Rfree = 0.000) for 11053 atoms. Found 22 (59 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11329 seeds are put forward NCS extension: 9 residues added (11 deleted due to clashes), 11338 seeds are put forward Round 1: 892 peptides, 118 chains. Longest chain 21 peptides. Score 0.550 Round 2: 935 peptides, 105 chains. Longest chain 28 peptides. Score 0.620 Round 3: 963 peptides, 97 chains. Longest chain 31 peptides. Score 0.659 Round 4: 929 peptides, 110 chains. Longest chain 28 peptides. Score 0.601 Round 5: 938 peptides, 112 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 3 Chains 104, Residues 866, Estimated correctness of the model 56.0 % 10 chains (189 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 22927 restraints for refining 11174 atoms. 18664 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2202 (Rfree = 0.000) for 11174 atoms. Found 60 (60 requested) and removed 62 (50 requested) atoms. Cycle 37: After refmac, R = 0.2049 (Rfree = 0.000) for 11141 atoms. Found 39 (60 requested) and removed 52 (50 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1988 (Rfree = 0.000) for 11117 atoms. Found 31 (59 requested) and removed 49 (49 requested) atoms. Cycle 39: After refmac, R = 0.1930 (Rfree = 0.000) for 11089 atoms. Found 22 (59 requested) and removed 50 (49 requested) atoms. Cycle 40: After refmac, R = 0.1882 (Rfree = 0.000) for 11058 atoms. Found 29 (59 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11336 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 11348 seeds are put forward Round 1: 854 peptides, 115 chains. Longest chain 37 peptides. Score 0.533 Round 2: 933 peptides, 97 chains. Longest chain 78 peptides. Score 0.642 Round 3: 924 peptides, 96 chains. Longest chain 39 peptides. Score 0.639 Round 4: 927 peptides, 102 chains. Longest chain 47 peptides. Score 0.623 Round 5: 937 peptides, 105 chains. Longest chain 40 peptides. Score 0.621 Taking the results from Round 2 Chains 104, Residues 836, Estimated correctness of the model 51.9 % 7 chains (155 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 23689 restraints for refining 11175 atoms. 19694 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2078 (Rfree = 0.000) for 11175 atoms. Found 60 (60 requested) and removed 59 (50 requested) atoms. Cycle 42: After refmac, R = 0.1996 (Rfree = 0.000) for 11158 atoms. Found 39 (60 requested) and removed 51 (50 requested) atoms. Cycle 43: After refmac, R = 0.1954 (Rfree = 0.000) for 11137 atoms. Found 24 (60 requested) and removed 50 (50 requested) atoms. Cycle 44: After refmac, R = 0.1897 (Rfree = 0.000) for 11106 atoms. Found 21 (59 requested) and removed 51 (49 requested) atoms. Cycle 45: After refmac, R = 0.1873 (Rfree = 0.000) for 11073 atoms. Found 22 (59 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11342 seeds are put forward NCS extension: 54 residues added (45 deleted due to clashes), 11396 seeds are put forward Round 1: 811 peptides, 112 chains. Longest chain 21 peptides. Score 0.510 Round 2: 912 peptides, 104 chains. Longest chain 30 peptides. Score 0.608 Round 3: 919 peptides, 106 chains. Longest chain 34 peptides. Score 0.606 Round 4: 899 peptides, 107 chains. Longest chain 24 peptides. Score 0.590 Round 5: 914 peptides, 100 chains. Longest chain 45 peptides. Score 0.621 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 103, Residues 814, Estimated correctness of the model 46.6 % 5 chains (122 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 104 B and 109 B 101 chains (816 residues) following loop building 4 chains (126 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29175 reflections ( 99.85 % complete ) and 24014 restraints for refining 11174 atoms. 20257 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2110 (Rfree = 0.000) for 11174 atoms. Found 0 (60 requested) and removed 32 (50 requested) atoms. Cycle 47: After refmac, R = 0.2002 (Rfree = 0.000) for 11121 atoms. Found 0 (59 requested) and removed 14 (49 requested) atoms. Cycle 48: After refmac, R = 0.1966 (Rfree = 0.000) for 11096 atoms. Found 0 (59 requested) and removed 22 (49 requested) atoms. Cycle 49: After refmac, R = 0.1938 (Rfree = 0.000) for 11065 atoms. Found 0 (59 requested) and removed 15 (49 requested) atoms. Writing output files ... TimeTaking 166.53