Sun 23 Dec 22:22:42 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 2gpj-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-2.2-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/2gpj-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-2.2-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 22:23:43 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/2gpj-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-2.2-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 283 and 0 Target number of residues in the AU: 283 Target solvent content: 0.5511 Checking the provided sequence file Detected sequence length: 252 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 252 Adjusted target solvent content: 0.60 Input MTZ file: 2gpj-2.2-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: 92 Cell parameters: 100.540 100.540 67.510 90.000 90.000 90.000 Input sequence file: 2gpj-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2016 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: 71.093 2.200 Wilson plot Bfac: 35.90 18094 reflections ( 99.85 % complete ) and 0 restraints for refining 2226 atoms. Observations/parameters ratio is 2.03 ------------------------------------------------------ Starting model: R = 0.3787 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3387 (Rfree = 0.000) for 2226 atoms. Found 52 (58 requested) and removed 39 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.56 2.24 Round 1: 141 peptides, 26 chains. Longest chain 15 peptides. Score 0.363 Round 2: 155 peptides, 24 chains. Longest chain 15 peptides. Score 0.467 Round 3: 160 peptides, 21 chains. Longest chain 22 peptides. Score 0.543 Round 4: 172 peptides, 20 chains. Longest chain 30 peptides. Score 0.604 Round 5: 171 peptides, 15 chains. Longest chain 48 peptides. Score 0.678 Taking the results from Round 5 Chains 16, Residues 156, Estimated correctness of the model 87.9 % 3 chains (74 residues) have been docked in sequence ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 3165 restraints for refining 1925 atoms. 2239 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3690 (Rfree = 0.000) for 1925 atoms. Found 50 (50 requested) and removed 30 (25 requested) atoms. Cycle 2: After refmac, R = 0.3506 (Rfree = 0.000) for 1937 atoms. Found 35 (50 requested) and removed 25 (25 requested) atoms. Cycle 3: After refmac, R = 0.3333 (Rfree = 0.000) for 1944 atoms. Found 17 (50 requested) and removed 25 (25 requested) atoms. Cycle 4: After refmac, R = 0.3257 (Rfree = 0.000) for 1930 atoms. Found 15 (50 requested) and removed 25 (25 requested) atoms. Cycle 5: After refmac, R = 0.3180 (Rfree = 0.000) for 1914 atoms. Found 10 (50 requested) and removed 14 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.44 2.13 Round 1: 172 peptides, 17 chains. Longest chain 42 peptides. Score 0.651 Round 2: 175 peptides, 12 chains. Longest chain 47 peptides. Score 0.731 Round 3: 188 peptides, 15 chains. Longest chain 42 peptides. Score 0.726 Round 4: 189 peptides, 15 chains. Longest chain 47 peptides. Score 0.728 Round 5: 188 peptides, 17 chains. Longest chain 28 peptides. Score 0.699 Taking the results from Round 2 Chains 14, Residues 163, Estimated correctness of the model 91.3 % 2 chains (69 residues) have been docked in sequence Building loops using Loopy2018 14 chains (163 residues) following loop building 2 chains (69 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 3363 restraints for refining 1949 atoms. 2437 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3359 (Rfree = 0.000) for 1949 atoms. Found 27 (50 requested) and removed 27 (25 requested) atoms. Cycle 7: After refmac, R = 0.3183 (Rfree = 0.000) for 1946 atoms. Found 24 (49 requested) and removed 14 (25 requested) atoms. Cycle 8: After refmac, R = 0.3066 (Rfree = 0.000) for 1951 atoms. Found 17 (49 requested) and removed 15 (25 requested) atoms. Cycle 9: After refmac, R = 0.2993 (Rfree = 0.000) for 1951 atoms. Found 11 (47 requested) and removed 9 (25 requested) atoms. Cycle 10: After refmac, R = 0.2937 (Rfree = 0.000) for 1952 atoms. Found 10 (46 requested) and removed 2 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.42 2.11 Round 1: 184 peptides, 15 chains. Longest chain 42 peptides. Score 0.715 Round 2: 181 peptides, 12 chains. Longest chain 42 peptides. Score 0.746 Round 3: 188 peptides, 13 chains. Longest chain 42 peptides. Score 0.751 Round 4: 192 peptides, 12 chains. Longest chain 55 peptides. Score 0.772 Round 5: 198 peptides, 15 chains. Longest chain 54 peptides. Score 0.751 Taking the results from Round 4 Chains 13, Residues 180, Estimated correctness of the model 93.6 % 4 chains (106 residues) have been docked in sequence Building loops using Loopy2018 13 chains (180 residues) following loop building 4 chains (106 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 2989 restraints for refining 1996 atoms. 1843 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3132 (Rfree = 0.000) for 1996 atoms. Found 48 (48 requested) and removed 28 (26 requested) atoms. Cycle 12: After refmac, R = 0.2985 (Rfree = 0.000) for 2016 atoms. Found 23 (47 requested) and removed 19 (26 requested) atoms. Cycle 13: After refmac, R = 0.2887 (Rfree = 0.000) for 2014 atoms. Found 20 (46 requested) and removed 15 (26 requested) atoms. Cycle 14: After refmac, R = 0.2822 (Rfree = 0.000) for 2017 atoms. Found 13 (45 requested) and removed 7 (26 requested) atoms. Cycle 15: After refmac, R = 0.2754 (Rfree = 0.000) for 2022 atoms. Found 12 (44 requested) and removed 4 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.44 2.13 Round 1: 198 peptides, 13 chains. Longest chain 54 peptides. Score 0.774 Round 2: 205 peptides, 11 chains. Longest chain 54 peptides. Score 0.810 Round 3: 196 peptides, 11 chains. Longest chain 57 peptides. Score 0.792 Round 4: 202 peptides, 14 chains. Longest chain 60 peptides. Score 0.771 Round 5: 209 peptides, 10 chains. Longest chain 60 peptides. Score 0.827 Taking the results from Round 5 Chains 11, Residues 199, Estimated correctness of the model 96.1 % 2 chains (78 residues) have been docked in sequence Building loops using Loopy2018 11 chains (199 residues) following loop building 2 chains (78 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 3243 restraints for refining 2031 atoms. 2109 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3071 (Rfree = 0.000) for 2031 atoms. Found 44 (45 requested) and removed 29 (26 requested) atoms. Cycle 17: After refmac, R = 0.2857 (Rfree = 0.000) for 2045 atoms. Found 22 (43 requested) and removed 26 (26 requested) atoms. Cycle 18: After refmac, R = 0.2733 (Rfree = 0.000) for 2040 atoms. Found 17 (42 requested) and removed 5 (26 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2661 (Rfree = 0.000) for 2052 atoms. Found 16 (42 requested) and removed 4 (26 requested) atoms. Cycle 20: After refmac, R = 0.2612 (Rfree = 0.000) for 2062 atoms. Found 11 (42 requested) and removed 9 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.41 2.11 Round 1: 201 peptides, 10 chains. Longest chain 55 peptides. Score 0.812 Round 2: 210 peptides, 8 chains. Longest chain 60 peptides. Score 0.847 Round 3: 209 peptides, 10 chains. Longest chain 57 peptides. Score 0.827 Round 4: 214 peptides, 11 chains. Longest chain 88 peptides. Score 0.826 Round 5: 217 peptides, 8 chains. Longest chain 95 peptides. Score 0.858 Taking the results from Round 5 Chains 9, Residues 209, Estimated correctness of the model 97.3 % 4 chains (159 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 188 A and 191 A Built loop between residues 213 A and 217 A 7 chains (214 residues) following loop building 2 chains (164 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 2591 restraints for refining 2115 atoms. 1046 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2832 (Rfree = 0.000) for 2115 atoms. Found 43 (43 requested) and removed 28 (27 requested) atoms. Cycle 22: After refmac, R = 0.2623 (Rfree = 0.000) for 2125 atoms. Found 35 (42 requested) and removed 27 (27 requested) atoms. Cycle 23: After refmac, R = 0.2486 (Rfree = 0.000) for 2127 atoms. Found 19 (41 requested) and removed 27 (27 requested) atoms. Cycle 24: After refmac, R = 0.2414 (Rfree = 0.000) for 2117 atoms. Found 23 (40 requested) and removed 18 (27 requested) atoms. Cycle 25: After refmac, R = 0.2358 (Rfree = 0.000) for 2117 atoms. Found 19 (38 requested) and removed 8 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.41 2.11 Round 1: 224 peptides, 8 chains. Longest chain 113 peptides. Score 0.868 Round 2: 231 peptides, 5 chains. Longest chain 129 peptides. Score 0.899 Round 3: 231 peptides, 5 chains. Longest chain 146 peptides. Score 0.899 Round 4: 226 peptides, 6 chains. Longest chain 96 peptides. Score 0.886 Round 5: 231 peptides, 5 chains. Longest chain 108 peptides. Score 0.899 Taking the results from Round 5 Chains 6, Residues 226, Estimated correctness of the model 98.6 % 4 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 84 A Built loop between residues 92 A and 103 A Built loop between residues 138 A and 141 A 2 chains (235 residues) following loop building 1 chains (215 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 2329 restraints for refining 2181 atoms. 497 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2615 (Rfree = 0.000) for 2181 atoms. Found 39 (39 requested) and removed 31 (28 requested) atoms. Cycle 27: After refmac, R = 0.2457 (Rfree = 0.000) for 2189 atoms. Found 39 (39 requested) and removed 28 (28 requested) atoms. Cycle 28: After refmac, R = 0.2325 (Rfree = 0.000) for 2197 atoms. Found 22 (38 requested) and removed 25 (28 requested) atoms. Cycle 29: After refmac, R = 0.2234 (Rfree = 0.000) for 2193 atoms. Found 34 (36 requested) and removed 16 (28 requested) atoms. Cycle 30: After refmac, R = 0.2161 (Rfree = 0.000) for 2208 atoms. Found 21 (36 requested) and removed 22 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.43 2.12 Round 1: 228 peptides, 5 chains. Longest chain 111 peptides. Score 0.895 Round 2: 234 peptides, 3 chains. Longest chain 146 peptides. Score 0.915 Round 3: 227 peptides, 6 chains. Longest chain 91 peptides. Score 0.887 Round 4: 234 peptides, 3 chains. Longest chain 146 peptides. Score 0.915 Round 5: 234 peptides, 5 chains. Longest chain 85 peptides. Score 0.902 Taking the results from Round 4 Chains 3, Residues 231, Estimated correctness of the model 98.9 % 3 chains (231 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 A and 34 A Built loop between residues 99 A and 103 A 1 chains (239 residues) following loop building 1 chains (239 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 2225 restraints for refining 2210 atoms. 282 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2345 (Rfree = 0.000) for 2210 atoms. Found 35 (35 requested) and removed 31 (28 requested) atoms. Cycle 32: After refmac, R = 0.2163 (Rfree = 0.000) for 2211 atoms. Found 33 (34 requested) and removed 22 (28 requested) atoms. Cycle 33: After refmac, R = 0.2087 (Rfree = 0.000) for 2221 atoms. Found 32 (33 requested) and removed 20 (28 requested) atoms. Cycle 34: After refmac, R = 0.2022 (Rfree = 0.000) for 2232 atoms. Found 32 (32 requested) and removed 18 (29 requested) atoms. Cycle 35: After refmac, R = 0.2010 (Rfree = 0.000) for 2245 atoms. Found 26 (31 requested) and removed 25 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.44 2.13 Round 1: 234 peptides, 4 chains. Longest chain 109 peptides. Score 0.909 Round 2: 234 peptides, 5 chains. Longest chain 91 peptides. Score 0.902 Round 3: 238 peptides, 4 chains. Longest chain 145 peptides. Score 0.912 Round 4: 235 peptides, 5 chains. Longest chain 108 peptides. Score 0.903 Round 5: 238 peptides, 3 chains. Longest chain 145 peptides. Score 0.919 Taking the results from Round 5 Chains 3, Residues 235, Estimated correctness of the model 99.0 % 3 chains (235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 37 A Built loop between residues 100 A and 104 A 1 chains (240 residues) following loop building 1 chains (240 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 18094 reflections ( 99.85 % complete ) and 2205 restraints for refining 2195 atoms. 254 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2227 (Rfree = 0.000) for 2195 atoms. Found 30 (30 requested) and removed 28 (28 requested) atoms. Cycle 37: After refmac, R = 0.2074 (Rfree = 0.000) for 2195 atoms. Found 28 (28 requested) and removed 13 (28 requested) atoms. Cycle 38: After refmac, R = 0.1995 (Rfree = 0.000) for 2210 atoms. Found 28 (28 requested) and removed 12 (28 requested) atoms. Cycle 39: After refmac, R = 0.1949 (Rfree = 0.000) for 2226 atoms. Found 29 (29 requested) and removed 20 (29 requested) atoms. Cycle 40: After refmac, R = 0.1919 (Rfree = 0.000) for 2234 atoms. Found 29 (29 requested) and removed 27 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.42 2.11 Round 1: 238 peptides, 3 chains. Longest chain 146 peptides. Score 0.919 Round 2: 239 peptides, 3 chains. Longest chain 129 peptides. Score 0.920 Round 3: 239 peptides, 3 chains. Longest chain 146 peptides. Score 0.920 Round 4: 236 peptides, 5 chains. Longest chain 108 peptides. Score 0.904 Round 5: 239 peptides, 3 chains. Longest chain 146 peptides. Score 0.920 Taking the results from Round 5 Chains 3, Residues 236, Estimated correctness of the model 99.1 % 3 chains (236 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 100 A and 103 A 1 chains (240 residues) following loop building 1 chains (240 residues) in sequence following loop building ------------------------------------------------------ 18094 reflections ( 99.85 % complete ) and 2190 restraints for refining 2180 atoms. 239 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2169 (Rfree = 0.000) for 2180 atoms. Found 28 (28 requested) and removed 26 (28 requested) atoms. Cycle 42: After refmac, R = 0.2048 (Rfree = 0.000) for 2180 atoms. Found 28 (28 requested) and removed 9 (28 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 2198 atoms. Found 28 (28 requested) and removed 18 (28 requested) atoms. Cycle 44: After refmac, R = 0.1944 (Rfree = 0.000) for 2206 atoms. Found 28 (28 requested) and removed 13 (28 requested) atoms. Cycle 45: After refmac, R = 0.1909 (Rfree = 0.000) for 2221 atoms. Found 28 (28 requested) and removed 19 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.43 2.12 Round 1: 237 peptides, 4 chains. Longest chain 108 peptides. Score 0.911 Round 2: 238 peptides, 3 chains. Longest chain 128 peptides. Score 0.919 Round 3: 237 peptides, 3 chains. Longest chain 115 peptides. Score 0.918 Round 4: 235 peptides, 5 chains. Longest chain 94 peptides. Score 0.903 Round 5: 230 peptides, 6 chains. Longest chain 59 peptides. Score 0.890 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 235, Estimated correctness of the model 99.0 % 3 chains (235 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 79 A and 82 A Built loop between residues 117 A and 120 A 1 chains (239 residues) following loop building 1 chains (239 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 18094 reflections ( 99.85 % complete ) and 1942 restraints for refining 1891 atoms. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2710 (Rfree = 0.000) for 1891 atoms. Found 23 (24 requested) and removed 0 (24 requested) atoms. Cycle 47: After refmac, R = 0.2506 (Rfree = 0.000) for 1891 atoms. Found 21 (24 requested) and removed 2 (24 requested) atoms. Cycle 48: After refmac, R = 0.2383 (Rfree = 0.000) for 1891 atoms. Found 9 (25 requested) and removed 3 (25 requested) atoms. Cycle 49: After refmac, R = 0.2315 (Rfree = 0.000) for 1891 atoms. TimeTaking 90.4