null Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hcf-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-1.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-1.8-parrot-hancs ############### 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 22:23:05 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/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-1.8-parrot-hancs/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 218 and 0 Target number of residues in the AU: 218 Target solvent content: 0.4753 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.44 Input MTZ file: 2hcf-1.8-parrot-hancs.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: 37.750 71.590 83.200 90.000 90.000 90.000 Input sequence file: 2hcf-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.40 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 54.266 1.800 Wilson plot Bfac: 18.38 21064 reflections ( 97.66 % complete ) and 0 restraints for refining 2080 atoms. Observations/parameters ratio is 2.53 ------------------------------------------------------ Starting model: R = 0.3387 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2960 (Rfree = 0.000) for 2080 atoms. Found 64 (96 requested) and removed 56 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.08 2.25 Round 1: 165 peptides, 18 chains. Longest chain 29 peptides. Score 0.735 Round 2: 186 peptides, 14 chains. Longest chain 33 peptides. Score 0.848 Round 3: 200 peptides, 10 chains. Longest chain 42 peptides. Score 0.907 Round 4: 199 peptides, 6 chains. Longest chain 97 peptides. Score 0.935 Round 5: 205 peptides, 6 chains. Longest chain 65 peptides. Score 0.940 Taking the results from Round 5 Chains 6, Residues 199, Estimated correctness of the model 99.7 % 3 chains (144 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 167 A 5 chains (203 residues) following loop building 2 chains (148 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 2257 restraints for refining 1848 atoms. 881 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3214 (Rfree = 0.000) for 1848 atoms. Found 60 (85 requested) and removed 43 (42 requested) atoms. Cycle 2: After refmac, R = 0.2932 (Rfree = 0.000) for 1859 atoms. Found 47 (84 requested) and removed 14 (43 requested) atoms. Cycle 3: After refmac, R = 0.2767 (Rfree = 0.000) for 1882 atoms. Found 40 (85 requested) and removed 7 (43 requested) atoms. Cycle 4: After refmac, R = 0.2618 (Rfree = 0.000) for 1910 atoms. Found 33 (86 requested) and removed 6 (44 requested) atoms. Cycle 5: After refmac, R = 0.2533 (Rfree = 0.000) for 1927 atoms. Found 39 (87 requested) and removed 5 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.87 2.03 Round 1: 209 peptides, 6 chains. Longest chain 58 peptides. Score 0.943 Round 2: 214 peptides, 4 chains. Longest chain 144 peptides. Score 0.958 Round 3: 213 peptides, 6 chains. Longest chain 77 peptides. Score 0.946 Round 4: 212 peptides, 5 chains. Longest chain 147 peptides. Score 0.951 Round 5: 215 peptides, 6 chains. Longest chain 60 peptides. Score 0.948 Taking the results from Round 2 Chains 4, Residues 210, Estimated correctness of the model 99.8 % 4 chains (210 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 22 A Built loop between residues 38 A and 47 A Built loop between residues 189 A and 192 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1900 restraints for refining 2003 atoms. 134 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2503 (Rfree = 0.000) for 2003 atoms. Found 54 (90 requested) and removed 48 (46 requested) atoms. Cycle 7: After refmac, R = 0.2329 (Rfree = 0.000) for 2007 atoms. Found 35 (88 requested) and removed 12 (46 requested) atoms. Cycle 8: After refmac, R = 0.2204 (Rfree = 0.000) for 2027 atoms. Found 43 (89 requested) and removed 14 (46 requested) atoms. Cycle 9: After refmac, R = 0.2120 (Rfree = 0.000) for 2050 atoms. Found 40 (91 requested) and removed 16 (47 requested) atoms. Cycle 10: After refmac, R = 0.2065 (Rfree = 0.000) for 2067 atoms. Found 45 (91 requested) and removed 9 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.86 2.02 Round 1: 217 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 2: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 3: 216 peptides, 4 chains. Longest chain 89 peptides. Score 0.959 Round 4: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 5: 215 peptides, 4 chains. Longest chain 121 peptides. Score 0.959 Taking the results from Round 4 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1914 restraints for refining 2043 atoms. 148 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2189 (Rfree = 0.000) for 2043 atoms. Found 57 (90 requested) and removed 37 (47 requested) atoms. Cycle 12: After refmac, R = 0.2053 (Rfree = 0.000) for 2063 atoms. Found 57 (89 requested) and removed 15 (47 requested) atoms. Cycle 13: After refmac, R = 0.1991 (Rfree = 0.000) for 2102 atoms. Found 48 (91 requested) and removed 12 (48 requested) atoms. Cycle 14: After refmac, R = 0.1946 (Rfree = 0.000) for 2134 atoms. Found 40 (92 requested) and removed 27 (49 requested) atoms. Cycle 15: After refmac, R = 0.1903 (Rfree = 0.000) for 2145 atoms. Found 46 (91 requested) and removed 27 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.86 2.02 Round 1: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 2: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 3: 216 peptides, 4 chains. Longest chain 89 peptides. Score 0.959 Round 4: 217 peptides, 3 chains. Longest chain 99 peptides. Score 0.965 Round 5: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Taking the results from Round 5 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1948 restraints for refining 2071 atoms. 182 conditional restraints added. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2097 (Rfree = 0.000) for 2071 atoms. Found 54 (85 requested) and removed 29 (47 requested) atoms. Cycle 17: After refmac, R = 0.2001 (Rfree = 0.000) for 2091 atoms. Found 45 (84 requested) and removed 10 (48 requested) atoms. Cycle 18: After refmac, R = 0.1926 (Rfree = 0.000) for 2126 atoms. Found 34 (86 requested) and removed 15 (49 requested) atoms. Cycle 19: After refmac, R = 0.1891 (Rfree = 0.000) for 2140 atoms. Found 40 (87 requested) and removed 23 (49 requested) atoms. Cycle 20: After refmac, R = 0.1863 (Rfree = 0.000) for 2154 atoms. Found 48 (85 requested) and removed 25 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.85 2.00 Round 1: 216 peptides, 4 chains. Longest chain 145 peptides. Score 0.959 Round 2: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 3: 217 peptides, 3 chains. Longest chain 128 peptides. Score 0.965 Round 4: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 5: 216 peptides, 4 chains. Longest chain 144 peptides. Score 0.959 Taking the results from Round 4 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1960 restraints for refining 2089 atoms. 194 conditional restraints added. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2058 (Rfree = 0.000) for 2089 atoms. Found 62 (81 requested) and removed 30 (48 requested) atoms. Cycle 22: After refmac, R = 0.1976 (Rfree = 0.000) for 2115 atoms. Found 44 (82 requested) and removed 15 (49 requested) atoms. Cycle 23: After refmac, R = 0.1908 (Rfree = 0.000) for 2143 atoms. Found 48 (83 requested) and removed 13 (49 requested) atoms. Cycle 24: After refmac, R = 0.1887 (Rfree = 0.000) for 2173 atoms. Found 35 (84 requested) and removed 37 (50 requested) atoms. Cycle 25: After refmac, R = 0.1878 (Rfree = 0.000) for 2166 atoms. Found 54 (82 requested) and removed 20 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.85 2.00 Round 1: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 2: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 3: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 4: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 5: 216 peptides, 4 chains. Longest chain 139 peptides. Score 0.959 Taking the results from Round 3 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1966 restraints for refining 2096 atoms. 200 conditional restraints added. Observations/parameters ratio is 2.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2026 (Rfree = 0.000) for 2096 atoms. Found 58 (79 requested) and removed 25 (48 requested) atoms. Cycle 27: After refmac, R = 0.1931 (Rfree = 0.000) for 2127 atoms. Found 42 (80 requested) and removed 19 (49 requested) atoms. Cycle 28: After refmac, R = 0.1878 (Rfree = 0.000) for 2146 atoms. Found 30 (81 requested) and removed 18 (49 requested) atoms. Cycle 29: After refmac, R = 0.1842 (Rfree = 0.000) for 2156 atoms. Found 36 (79 requested) and removed 11 (49 requested) atoms. Cycle 30: After refmac, R = 0.1841 (Rfree = 0.000) for 2178 atoms. Found 34 (80 requested) and removed 25 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.85 2.00 Round 1: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 2: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 3: 216 peptides, 4 chains. Longest chain 128 peptides. Score 0.959 Round 4: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 5: 216 peptides, 4 chains. Longest chain 138 peptides. Score 0.959 Taking the results from Round 4 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1990 restraints for refining 2110 atoms. 224 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2010 (Rfree = 0.000) for 2110 atoms. Found 64 (76 requested) and removed 24 (48 requested) atoms. Cycle 32: After refmac, R = 0.1940 (Rfree = 0.000) for 2149 atoms. Found 33 (77 requested) and removed 18 (49 requested) atoms. Cycle 33: After refmac, R = 0.1865 (Rfree = 0.000) for 2163 atoms. Found 32 (76 requested) and removed 7 (50 requested) atoms. Cycle 34: After refmac, R = 0.1846 (Rfree = 0.000) for 2186 atoms. Found 24 (77 requested) and removed 18 (50 requested) atoms. Cycle 35: After refmac, R = 0.1813 (Rfree = 0.000) for 2189 atoms. Found 40 (75 requested) and removed 19 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.85 2.00 Round 1: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 2: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 3: 218 peptides, 3 chains. Longest chain 185 peptides. Score 0.965 Round 4: 219 peptides, 3 chains. Longest chain 128 peptides. Score 0.966 Round 5: 217 peptides, 3 chains. Longest chain 170 peptides. Score 0.965 Taking the results from Round 2 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1980 restraints for refining 2110 atoms. 214 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2012 (Rfree = 0.000) for 2110 atoms. Found 67 (72 requested) and removed 26 (48 requested) atoms. Cycle 37: After refmac, R = 0.1956 (Rfree = 0.000) for 2149 atoms. Found 35 (73 requested) and removed 18 (49 requested) atoms. Cycle 38: After refmac, R = 0.1876 (Rfree = 0.000) for 2166 atoms. Found 40 (72 requested) and removed 15 (50 requested) atoms. Cycle 39: After refmac, R = 0.1858 (Rfree = 0.000) for 2186 atoms. Found 29 (73 requested) and removed 23 (50 requested) atoms. Cycle 40: After refmac, R = 0.1827 (Rfree = 0.000) for 2190 atoms. Found 33 (71 requested) and removed 18 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.85 2.00 Round 1: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 2: 217 peptides, 3 chains. Longest chain 184 peptides. Score 0.965 Round 3: 217 peptides, 3 chains. Longest chain 145 peptides. Score 0.965 Round 4: 216 peptides, 4 chains. Longest chain 128 peptides. Score 0.959 Round 5: 215 peptides, 5 chains. Longest chain 130 peptides. Score 0.953 Taking the results from Round 1 Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 21064 reflections ( 97.66 % complete ) and 1999 restraints for refining 2118 atoms. 233 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2006 (Rfree = 0.000) for 2118 atoms. Found 66 (66 requested) and removed 20 (48 requested) atoms. Cycle 42: After refmac, R = 0.1956 (Rfree = 0.000) for 2162 atoms. Found 33 (68 requested) and removed 23 (50 requested) atoms. Cycle 43: After refmac, R = 0.1894 (Rfree = 0.000) for 2169 atoms. Found 44 (66 requested) and removed 16 (50 requested) atoms. Cycle 44: After refmac, R = 0.1886 (Rfree = 0.000) for 2195 atoms. Found 25 (67 requested) and removed 29 (50 requested) atoms. Cycle 45: After refmac, R = 0.1869 (Rfree = 0.000) for 2185 atoms. Found 51 (65 requested) and removed 18 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.85 2.00 Round 1: 216 peptides, 4 chains. Longest chain 145 peptides. Score 0.959 Round 2: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 3: 211 peptides, 5 chains. Longest chain 89 peptides. Score 0.951 Round 4: 218 peptides, 2 chains. Longest chain 184 peptides. Score 0.970 Round 5: 216 peptides, 4 chains. Longest chain 154 peptides. Score 0.959 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 216, Estimated correctness of the model 99.9 % 2 chains (216 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 38 A and 46 A 1 chains (223 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 21064 reflections ( 97.66 % complete ) and 1766 restraints for refining 1740 atoms. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2633 (Rfree = 0.000) for 1740 atoms. Found 37 (51 requested) and removed 0 (51 requested) atoms. Cycle 47: After refmac, R = 0.2423 (Rfree = 0.000) for 1740 atoms. Found 13 (52 requested) and removed 0 (41 requested) atoms. Cycle 48: After refmac, R = 0.2315 (Rfree = 0.000) for 1740 atoms. Found 10 (52 requested) and removed 1 (41 requested) atoms. Cycle 49: After refmac, R = 0.2253 (Rfree = 0.000) for 1740 atoms. Found 10 (53 requested) and removed 0 (41 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:12 GMT 2018 Job finished. TimeTaking 47.27 Used memory is bytes: 12195368