null Sun 23 Dec 22:22:59 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 2ess-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ess-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ess-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-1.9-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/2ess-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-1.9-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 22:23:08 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/2ess-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-1.9-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 273 and 0 Target number of residues in the AU: 273 Target solvent content: 0.5245 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.57 Input MTZ file: 2ess-1.9-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: 152 Cell parameters: 91.150 91.150 64.770 90.000 90.000 120.000 Input sequence file: 2ess-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.60 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: 29.962 1.901 Wilson plot Bfac: 28.80 24679 reflections ( 99.57 % complete ) and 0 restraints for refining 2196 atoms. Observations/parameters ratio is 2.81 ------------------------------------------------------ Starting model: R = 0.3741 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3323 (Rfree = 0.000) for 2196 atoms. Found 31 (86 requested) and removed 47 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.15 Round 1: 163 peptides, 18 chains. Longest chain 19 peptides. Score 0.632 Round 2: 188 peptides, 16 chains. Longest chain 23 peptides. Score 0.740 Round 3: 202 peptides, 10 chains. Longest chain 34 peptides. Score 0.839 Round 4: 205 peptides, 7 chains. Longest chain 61 peptides. Score 0.871 Round 5: 207 peptides, 12 chains. Longest chain 35 peptides. Score 0.828 Taking the results from Round 4 Chains 8, Residues 198, Estimated correctness of the model 98.6 % 3 chains (143 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 73 A 7 chains (205 residues) following loop building 2 chains (150 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2674 restraints for refining 2066 atoms. 1188 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3338 (Rfree = 0.000) for 2066 atoms. Found 63 (81 requested) and removed 34 (40 requested) atoms. Cycle 2: After refmac, R = 0.3000 (Rfree = 0.000) for 2082 atoms. Found 47 (80 requested) and removed 27 (41 requested) atoms. Cycle 3: After refmac, R = 0.2850 (Rfree = 0.000) for 2078 atoms. Found 51 (80 requested) and removed 19 (41 requested) atoms. Cycle 4: After refmac, R = 0.2680 (Rfree = 0.000) for 2088 atoms. Found 43 (80 requested) and removed 17 (41 requested) atoms. Cycle 5: After refmac, R = 0.2549 (Rfree = 0.000) for 2103 atoms. Found 49 (80 requested) and removed 8 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.17 1.98 Round 1: 224 peptides, 6 chains. Longest chain 103 peptides. Score 0.903 Round 2: 221 peptides, 7 chains. Longest chain 117 peptides. Score 0.893 Round 3: 223 peptides, 6 chains. Longest chain 71 peptides. Score 0.902 Round 4: 221 peptides, 4 chains. Longest chain 117 peptides. Score 0.914 Round 5: 224 peptides, 5 chains. Longest chain 118 peptides. Score 0.910 Taking the results from Round 4 Chains 4, Residues 217, Estimated correctness of the model 99.3 % 3 chains (211 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 167 A 3 chains (221 residues) following loop building 2 chains (215 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2271 restraints for refining 2139 atoms. 445 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2452 (Rfree = 0.000) for 2139 atoms. Found 69 (81 requested) and removed 45 (42 requested) atoms. Cycle 7: After refmac, R = 0.2240 (Rfree = 0.000) for 2160 atoms. Found 56 (80 requested) and removed 17 (42 requested) atoms. Cycle 8: After refmac, R = 0.2122 (Rfree = 0.000) for 2190 atoms. Found 43 (81 requested) and removed 13 (43 requested) atoms. Cycle 9: After refmac, R = 0.2014 (Rfree = 0.000) for 2208 atoms. Found 38 (82 requested) and removed 19 (43 requested) atoms. Cycle 10: After refmac, R = 0.1959 (Rfree = 0.000) for 2224 atoms. Found 33 (83 requested) and removed 14 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.14 1.95 Round 1: 223 peptides, 8 chains. Longest chain 64 peptides. Score 0.888 Round 2: 226 peptides, 6 chains. Longest chain 68 peptides. Score 0.906 Round 3: 231 peptides, 3 chains. Longest chain 113 peptides. Score 0.930 Round 4: 229 peptides, 4 chains. Longest chain 90 peptides. Score 0.922 Round 5: 230 peptides, 4 chains. Longest chain 100 peptides. Score 0.923 Taking the results from Round 3 Chains 3, Residues 228, Estimated correctness of the model 99.5 % 3 chains (228 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A 2 chains (230 residues) following loop building 2 chains (230 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2202 restraints for refining 2180 atoms. 284 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2169 (Rfree = 0.000) for 2180 atoms. Found 58 (81 requested) and removed 48 (43 requested) atoms. Cycle 12: After refmac, R = 0.1999 (Rfree = 0.000) for 2188 atoms. Found 40 (79 requested) and removed 12 (43 requested) atoms. Cycle 13: After refmac, R = 0.1913 (Rfree = 0.000) for 2213 atoms. Found 37 (80 requested) and removed 15 (43 requested) atoms. Cycle 14: After refmac, R = 0.1860 (Rfree = 0.000) for 2229 atoms. Found 33 (81 requested) and removed 13 (44 requested) atoms. Cycle 15: After refmac, R = 0.1824 (Rfree = 0.000) for 2242 atoms. Found 30 (82 requested) and removed 19 (44 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.14 1.95 Round 1: 227 peptides, 6 chains. Longest chain 66 peptides. Score 0.907 Round 2: 229 peptides, 5 chains. Longest chain 90 peptides. Score 0.915 Round 3: 231 peptides, 3 chains. Longest chain 119 peptides. Score 0.930 Round 4: 230 peptides, 4 chains. Longest chain 119 peptides. Score 0.923 Round 5: 225 peptides, 5 chains. Longest chain 86 peptides. Score 0.911 Taking the results from Round 3 Chains 3, Residues 228, Estimated correctness of the model 99.5 % 3 chains (228 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 191 A and 194 A 2 chains (230 residues) following loop building 2 chains (230 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2221 restraints for refining 2190 atoms. 303 conditional restraints added. Observations/parameters ratio is 2.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2095 (Rfree = 0.000) for 2190 atoms. Found 52 (77 requested) and removed 51 (43 requested) atoms. Cycle 17: After refmac, R = 0.1931 (Rfree = 0.000) for 2190 atoms. Found 38 (76 requested) and removed 19 (43 requested) atoms. Cycle 18: After refmac, R = 0.1875 (Rfree = 0.000) for 2205 atoms. Found 36 (77 requested) and removed 17 (43 requested) atoms. Cycle 19: After refmac, R = 0.1830 (Rfree = 0.000) for 2223 atoms. Found 34 (77 requested) and removed 17 (44 requested) atoms. Cycle 20: After refmac, R = 0.1800 (Rfree = 0.000) for 2236 atoms. Found 41 (77 requested) and removed 15 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.14 1.95 Round 1: 230 peptides, 6 chains. Longest chain 85 peptides. Score 0.910 Round 2: 231 peptides, 4 chains. Longest chain 90 peptides. Score 0.924 Round 3: 224 peptides, 5 chains. Longest chain 86 peptides. Score 0.910 Round 4: 234 peptides, 3 chains. Longest chain 121 peptides. Score 0.932 Round 5: 226 peptides, 7 chains. Longest chain 80 peptides. Score 0.898 Taking the results from Round 4 Chains 4, Residues 231, Estimated correctness of the model 99.6 % 3 chains (230 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 223 A and 227 A 2 chains (233 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2184 restraints for refining 2195 atoms. 234 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2006 (Rfree = 0.000) for 2195 atoms. Found 62 (76 requested) and removed 32 (43 requested) atoms. Cycle 22: After refmac, R = 0.1875 (Rfree = 0.000) for 2220 atoms. Found 37 (76 requested) and removed 17 (44 requested) atoms. Cycle 23: After refmac, R = 0.1815 (Rfree = 0.000) for 2237 atoms. Found 41 (76 requested) and removed 18 (44 requested) atoms. Cycle 24: After refmac, R = 0.1764 (Rfree = 0.000) for 2257 atoms. Found 35 (77 requested) and removed 20 (44 requested) atoms. Cycle 25: After refmac, R = 0.1739 (Rfree = 0.000) for 2266 atoms. Found 50 (75 requested) and removed 22 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 1.94 Round 1: 235 peptides, 4 chains. Longest chain 102 peptides. Score 0.927 Round 2: 232 peptides, 3 chains. Longest chain 114 peptides. Score 0.931 Round 3: 231 peptides, 3 chains. Longest chain 113 peptides. Score 0.930 Round 4: 232 peptides, 4 chains. Longest chain 119 peptides. Score 0.925 Round 5: 231 peptides, 3 chains. Longest chain 118 peptides. Score 0.930 Taking the results from Round 2 Chains 3, Residues 229, Estimated correctness of the model 99.5 % 3 chains (229 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A 2 chains (231 residues) following loop building 2 chains (231 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2209 restraints for refining 2194 atoms. 279 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1968 (Rfree = 0.000) for 2194 atoms. Found 61 (72 requested) and removed 26 (43 requested) atoms. Cycle 27: After refmac, R = 0.1861 (Rfree = 0.000) for 2227 atoms. Found 40 (74 requested) and removed 17 (44 requested) atoms. Cycle 28: After refmac, R = 0.1800 (Rfree = 0.000) for 2246 atoms. Found 26 (75 requested) and removed 14 (44 requested) atoms. Cycle 29: After refmac, R = 0.1757 (Rfree = 0.000) for 2249 atoms. Found 36 (73 requested) and removed 15 (44 requested) atoms. Cycle 30: After refmac, R = 0.1733 (Rfree = 0.000) for 2266 atoms. Found 31 (73 requested) and removed 20 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.14 1.95 Round 1: 231 peptides, 4 chains. Longest chain 119 peptides. Score 0.924 Round 2: 231 peptides, 4 chains. Longest chain 109 peptides. Score 0.924 Round 3: 232 peptides, 3 chains. Longest chain 114 peptides. Score 0.931 Round 4: 232 peptides, 3 chains. Longest chain 119 peptides. Score 0.931 Round 5: 229 peptides, 2 chains. Longest chain 119 peptides. Score 0.934 Taking the results from Round 5 Chains 2, Residues 227, Estimated correctness of the model 99.6 % 2 chains (227 residues) have been docked in sequence Building loops using Loopy2018 2 chains (227 residues) following loop building 2 chains (227 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2269 restraints for refining 2178 atoms. 375 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1963 (Rfree = 0.000) for 2178 atoms. Found 61 (69 requested) and removed 24 (43 requested) atoms. Cycle 32: After refmac, R = 0.1842 (Rfree = 0.000) for 2212 atoms. Found 39 (70 requested) and removed 13 (43 requested) atoms. Cycle 33: After refmac, R = 0.1790 (Rfree = 0.000) for 2235 atoms. Found 32 (70 requested) and removed 16 (44 requested) atoms. Cycle 34: After refmac, R = 0.1759 (Rfree = 0.000) for 2246 atoms. Found 32 (71 requested) and removed 18 (44 requested) atoms. Cycle 35: After refmac, R = 0.1732 (Rfree = 0.000) for 2256 atoms. Found 39 (69 requested) and removed 17 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.14 1.95 Round 1: 232 peptides, 4 chains. Longest chain 121 peptides. Score 0.925 Round 2: 232 peptides, 3 chains. Longest chain 119 peptides. Score 0.931 Round 3: 233 peptides, 2 chains. Longest chain 119 peptides. Score 0.938 Round 4: 232 peptides, 2 chains. Longest chain 118 peptides. Score 0.937 Round 5: 229 peptides, 3 chains. Longest chain 120 peptides. Score 0.928 Taking the results from Round 3 Chains 2, Residues 231, Estimated correctness of the model 99.6 % 2 chains (231 residues) have been docked in sequence Building loops using Loopy2018 2 chains (231 residues) following loop building 2 chains (231 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2227 restraints for refining 2192 atoms. 297 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1946 (Rfree = 0.000) for 2192 atoms. Found 67 (67 requested) and removed 27 (43 requested) atoms. Cycle 37: After refmac, R = 0.1847 (Rfree = 0.000) for 2228 atoms. Found 44 (69 requested) and removed 18 (44 requested) atoms. Cycle 38: After refmac, R = 0.1796 (Rfree = 0.000) for 2251 atoms. Found 47 (69 requested) and removed 20 (44 requested) atoms. Cycle 39: After refmac, R = 0.1749 (Rfree = 0.000) for 2273 atoms. Found 42 (70 requested) and removed 25 (45 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 2284 atoms. Found 36 (68 requested) and removed 20 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.14 1.95 Round 1: 230 peptides, 4 chains. Longest chain 76 peptides. Score 0.923 Round 2: 235 peptides, 3 chains. Longest chain 122 peptides. Score 0.933 Round 3: 234 peptides, 2 chains. Longest chain 120 peptides. Score 0.938 Round 4: 235 peptides, 3 chains. Longest chain 122 peptides. Score 0.933 Round 5: 232 peptides, 4 chains. Longest chain 101 peptides. Score 0.925 Taking the results from Round 3 Chains 2, Residues 232, Estimated correctness of the model 99.6 % 2 chains (232 residues) have been docked in sequence Building loops using Loopy2018 2 chains (232 residues) following loop building 2 chains (232 residues) in sequence following loop building ------------------------------------------------------ 24679 reflections ( 99.57 % complete ) and 2226 restraints for refining 2197 atoms. 290 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1951 (Rfree = 0.000) for 2197 atoms. Found 64 (64 requested) and removed 28 (43 requested) atoms. Cycle 42: After refmac, R = 0.1840 (Rfree = 0.000) for 2228 atoms. Found 52 (65 requested) and removed 15 (44 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 2264 atoms. Found 33 (66 requested) and removed 21 (44 requested) atoms. Cycle 44: After refmac, R = 0.1742 (Rfree = 0.000) for 2270 atoms. Found 35 (65 requested) and removed 20 (45 requested) atoms. Cycle 45: After refmac, R = 0.1707 (Rfree = 0.000) for 2281 atoms. Found 36 (63 requested) and removed 23 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.14 1.95 Round 1: 230 peptides, 5 chains. Longest chain 67 peptides. Score 0.916 Round 2: 231 peptides, 5 chains. Longest chain 81 peptides. Score 0.917 Round 3: 232 peptides, 4 chains. Longest chain 101 peptides. Score 0.925 Round 4: 233 peptides, 3 chains. Longest chain 114 peptides. Score 0.932 Round 5: 232 peptides, 4 chains. Longest chain 120 peptides. Score 0.925 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 230, Estimated correctness of the model 99.6 % 3 chains (230 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 68 A and 71 A Built loop between residues 121 A and 135 A 1 chains (245 residues) following loop building 1 chains (245 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 24679 reflections ( 99.57 % complete ) and 2032 restraints for refining 1985 atoms. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2566 (Rfree = 0.000) for 1985 atoms. Found 32 (53 requested) and removed 0 (53 requested) atoms. Cycle 47: After refmac, R = 0.2299 (Rfree = 0.000) for 1985 atoms. Found 20 (54 requested) and removed 1 (39 requested) atoms. Cycle 48: After refmac, R = 0.2158 (Rfree = 0.000) for 1985 atoms. Found 9 (54 requested) and removed 1 (40 requested) atoms. Cycle 49: After refmac, R = 0.2074 (Rfree = 0.000) for 1985 atoms. Found 10 (54 requested) and removed 4 (40 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:26 GMT 2018 Job finished. TimeTaking 51.45 Used memory is bytes: 20105944