Tue 25 Dec 19:27:57 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 2huj-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huj-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huj-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-2.0-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/2huj-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-2.0-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 ============================================================ Tue 25 Dec 19:28:07 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/2huj-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-2.0-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 176 and 0 Target number of residues in the AU: 176 Target solvent content: 0.5054 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.61 Input MTZ file: 2huj-2.0-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: 182 Cell parameters: 100.110 100.110 66.570 90.000 90.000 120.000 Input sequence file: 2huj-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.50 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: 86.698 2.000 Wilson plot Bfac: 24.33 13789 reflections ( 99.93 % complete ) and 0 restraints for refining 1237 atoms. Observations/parameters ratio is 2.79 ------------------------------------------------------ Starting model: R = 0.3266 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2732 (Rfree = 0.000) for 1237 atoms. Found 42 (42 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.08 1.79 Round 1: 100 peptides, 12 chains. Longest chain 21 peptides. Score 0.602 Round 2: 110 peptides, 5 chains. Longest chain 49 peptides. Score 0.812 Round 3: 118 peptides, 4 chains. Longest chain 79 peptides. Score 0.854 Round 4: 121 peptides, 2 chains. Longest chain 71 peptides. Score 0.890 Round 5: 120 peptides, 3 chains. Longest chain 59 peptides. Score 0.874 Taking the results from Round 4 Chains 2, Residues 119, Estimated correctness of the model 98.8 % 2 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 67 A 1 chains (121 residues) following loop building 1 chains (121 residues) in sequence following loop building ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1143 restraints for refining 1165 atoms. 82 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2788 (Rfree = 0.000) for 1165 atoms. Found 39 (39 requested) and removed 21 (19 requested) atoms. Cycle 2: After refmac, R = 0.2421 (Rfree = 0.000) for 1181 atoms. Found 39 (39 requested) and removed 21 (20 requested) atoms. Cycle 3: After refmac, R = 0.2222 (Rfree = 0.000) for 1191 atoms. Found 39 (39 requested) and removed 14 (20 requested) atoms. Cycle 4: After refmac, R = 0.2107 (Rfree = 0.000) for 1208 atoms. Found 38 (39 requested) and removed 12 (20 requested) atoms. Cycle 5: After refmac, R = 0.2006 (Rfree = 0.000) for 1225 atoms. Found 32 (40 requested) and removed 12 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.05 1.77 Round 1: 119 peptides, 2 chains. Longest chain 69 peptides. Score 0.886 Round 2: 121 peptides, 3 chains. Longest chain 108 peptides. Score 0.876 Round 3: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 4: 119 peptides, 3 chains. Longest chain 83 peptides. Score 0.871 Round 5: 122 peptides, 1 chains. Longest chain 122 peptides. Score 0.905 Taking the results from Round 5 Chains 1, Residues 121, Estimated correctness of the model 99.0 % 1 chains (121 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1147 restraints for refining 1196 atoms. 86 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2139 (Rfree = 0.000) for 1196 atoms. Found 38 (38 requested) and removed 20 (20 requested) atoms. Cycle 7: After refmac, R = 0.1982 (Rfree = 0.000) for 1211 atoms. Found 33 (39 requested) and removed 18 (20 requested) atoms. Cycle 8: After refmac, R = 0.1893 (Rfree = 0.000) for 1224 atoms. Found 39 (39 requested) and removed 14 (21 requested) atoms. Cycle 9: After refmac, R = 0.1852 (Rfree = 0.000) for 1245 atoms. Found 26 (39 requested) and removed 20 (21 requested) atoms. Cycle 10: After refmac, R = 0.1805 (Rfree = 0.000) for 1247 atoms. Found 25 (38 requested) and removed 12 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.05 1.77 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 3: 121 peptides, 3 chains. Longest chain 108 peptides. Score 0.876 Round 4: 121 peptides, 3 chains. Longest chain 82 peptides. Score 0.876 Round 5: 121 peptides, 2 chains. Longest chain 76 peptides. Score 0.890 Taking the results from Round 2 Chains 1, Residues 120, Estimated correctness of the model 99.0 % 1 chains (120 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1167 restraints for refining 1229 atoms. 115 conditional restraints added. Observations/parameters ratio is 2.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1950 (Rfree = 0.000) for 1229 atoms. Found 37 (38 requested) and removed 21 (21 requested) atoms. Cycle 12: After refmac, R = 0.1865 (Rfree = 0.000) for 1243 atoms. Found 25 (37 requested) and removed 17 (21 requested) atoms. Cycle 13: After refmac, R = 0.1801 (Rfree = 0.000) for 1249 atoms. Found 36 (36 requested) and removed 8 (21 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1758 (Rfree = 0.000) for 1277 atoms. Found 24 (37 requested) and removed 21 (21 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1738 (Rfree = 0.000) for 1277 atoms. Found 33 (36 requested) and removed 16 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.05 1.77 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 120 peptides, 2 chains. Longest chain 115 peptides. Score 0.888 Round 3: 118 peptides, 2 chains. Longest chain 111 peptides. Score 0.884 Round 4: 120 peptides, 3 chains. Longest chain 76 peptides. Score 0.874 Round 5: 122 peptides, 1 chains. Longest chain 122 peptides. Score 0.905 Taking the results from Round 5 Chains 1, Residues 121, Estimated correctness of the model 99.0 % 1 chains (121 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1163 restraints for refining 1221 atoms. 102 conditional restraints added. Observations/parameters ratio is 2.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2006 (Rfree = 0.000) for 1221 atoms. Found 34 (34 requested) and removed 20 (20 requested) atoms. Cycle 17: After refmac, R = 0.1880 (Rfree = 0.000) for 1231 atoms. Found 34 (34 requested) and removed 16 (21 requested) atoms. Cycle 18: After refmac, R = 0.1806 (Rfree = 0.000) for 1247 atoms. Found 34 (34 requested) and removed 18 (21 requested) atoms. Cycle 19: After refmac, R = 0.1783 (Rfree = 0.000) for 1262 atoms. Found 29 (34 requested) and removed 23 (21 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1781 (Rfree = 0.000) for 1265 atoms. Found 32 (34 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.04 1.76 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 122 peptides, 2 chains. Longest chain 114 peptides. Score 0.892 Round 3: 121 peptides, 2 chains. Longest chain 116 peptides. Score 0.890 Round 4: 122 peptides, 2 chains. Longest chain 88 peptides. Score 0.892 Round 5: 120 peptides, 4 chains. Longest chain 68 peptides. Score 0.859 Taking the results from Round 1 Chains 1, Residues 120, Estimated correctness of the model 99.0 % 1 chains (120 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1168 restraints for refining 1211 atoms. 116 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1964 (Rfree = 0.000) for 1211 atoms. Found 31 (31 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1840 (Rfree = 0.000) for 1220 atoms. Found 30 (30 requested) and removed 14 (20 requested) atoms. Cycle 23: After refmac, R = 0.1782 (Rfree = 0.000) for 1235 atoms. Found 26 (31 requested) and removed 11 (21 requested) atoms. Cycle 24: After refmac, R = 0.1781 (Rfree = 0.000) for 1250 atoms. Found 30 (31 requested) and removed 19 (21 requested) atoms. Cycle 25: After refmac, R = 0.1749 (Rfree = 0.000) for 1260 atoms. Found 31 (31 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.05 1.77 Round 1: 122 peptides, 1 chains. Longest chain 122 peptides. Score 0.905 Round 2: 121 peptides, 2 chains. Longest chain 114 peptides. Score 0.890 Round 3: 121 peptides, 2 chains. Longest chain 116 peptides. Score 0.890 Round 4: 121 peptides, 2 chains. Longest chain 76 peptides. Score 0.890 Round 5: 121 peptides, 2 chains. Longest chain 114 peptides. Score 0.890 Taking the results from Round 1 Chains 1, Residues 121, Estimated correctness of the model 99.0 % 1 chains (121 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1158 restraints for refining 1216 atoms. 97 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1966 (Rfree = 0.000) for 1216 atoms. Found 29 (29 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1831 (Rfree = 0.000) for 1223 atoms. Found 28 (28 requested) and removed 19 (20 requested) atoms. Cycle 28: After refmac, R = 0.1775 (Rfree = 0.000) for 1232 atoms. Found 28 (28 requested) and removed 12 (21 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1748 (Rfree = 0.000) for 1247 atoms. Found 28 (28 requested) and removed 15 (21 requested) atoms. Cycle 30: After refmac, R = 0.1720 (Rfree = 0.000) for 1258 atoms. Found 28 (28 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.03 1.75 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 3: 120 peptides, 3 chains. Longest chain 108 peptides. Score 0.874 Round 4: 121 peptides, 2 chains. Longest chain 76 peptides. Score 0.890 Round 5: 121 peptides, 2 chains. Longest chain 116 peptides. Score 0.890 Taking the results from Round 2 Chains 1, Residues 120, Estimated correctness of the model 99.0 % 1 chains (120 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1166 restraints for refining 1220 atoms. 114 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1940 (Rfree = 0.000) for 1220 atoms. Found 25 (25 requested) and removed 21 (20 requested) atoms. Cycle 32: After refmac, R = 0.1825 (Rfree = 0.000) for 1224 atoms. Found 25 (25 requested) and removed 15 (20 requested) atoms. Cycle 33: After refmac, R = 0.1763 (Rfree = 0.000) for 1234 atoms. Found 24 (24 requested) and removed 13 (21 requested) atoms. Cycle 34: After refmac, R = 0.1739 (Rfree = 0.000) for 1245 atoms. Found 24 (24 requested) and removed 20 (21 requested) atoms. Cycle 35: After refmac, R = 0.1720 (Rfree = 0.000) for 1246 atoms. Found 23 (23 requested) and removed 18 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.04 1.76 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 3: 119 peptides, 4 chains. Longest chain 73 peptides. Score 0.856 Round 4: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 5: 120 peptides, 4 chains. Longest chain 68 peptides. Score 0.859 Taking the results from Round 4 Chains 1, Residues 120, Estimated correctness of the model 99.0 % 1 chains (120 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1168 restraints for refining 1210 atoms. 116 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1960 (Rfree = 0.000) for 1210 atoms. Found 21 (21 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1830 (Rfree = 0.000) for 1209 atoms. Found 20 (20 requested) and removed 11 (20 requested) atoms. Cycle 38: After refmac, R = 0.1774 (Rfree = 0.000) for 1218 atoms. Found 20 (20 requested) and removed 14 (20 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1756 (Rfree = 0.000) for 1224 atoms. Found 20 (20 requested) and removed 14 (20 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1738 (Rfree = 0.000) for 1230 atoms. Found 21 (21 requested) and removed 20 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.03 1.75 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 3: 120 peptides, 3 chains. Longest chain 108 peptides. Score 0.874 Round 4: 119 peptides, 3 chains. Longest chain 75 peptides. Score 0.871 Round 5: 121 peptides, 2 chains. Longest chain 114 peptides. Score 0.890 Taking the results from Round 2 Chains 1, Residues 120, Estimated correctness of the model 99.0 % 1 chains (120 residues) have been docked in sequence ------------------------------------------------------ 13789 reflections ( 99.93 % complete ) and 1141 restraints for refining 1195 atoms. 89 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1965 (Rfree = 0.000) for 1195 atoms. Found 20 (20 requested) and removed 20 (20 requested) atoms. Cycle 42: After refmac, R = 0.1869 (Rfree = 0.000) for 1195 atoms. Found 20 (20 requested) and removed 12 (20 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1792 (Rfree = 0.000) for 1203 atoms. Found 20 (20 requested) and removed 7 (20 requested) atoms. Cycle 44: After refmac, R = 0.1773 (Rfree = 0.000) for 1216 atoms. Found 20 (20 requested) and removed 15 (20 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1741 (Rfree = 0.000) for 1221 atoms. Found 20 (20 requested) and removed 14 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.03 1.75 Round 1: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 2: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Round 3: 120 peptides, 3 chains. Longest chain 108 peptides. Score 0.874 Round 4: 120 peptides, 2 chains. Longest chain 75 peptides. Score 0.888 Round 5: 121 peptides, 1 chains. Longest chain 121 peptides. Score 0.904 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 120, Estimated correctness of the model 99.0 % 1 chains (120 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 13789 reflections ( 99.93 % complete ) and 1052 restraints for refining 1026 atoms. Observations/parameters ratio is 3.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2519 (Rfree = 0.000) for 1026 atoms. Found 17 (17 requested) and removed 0 (17 requested) atoms. Cycle 47: After refmac, R = 0.2295 (Rfree = 0.000) for 1026 atoms. Found 17 (17 requested) and removed 0 (17 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2163 (Rfree = 0.000) for 1026 atoms. Found 13 (18 requested) and removed 1 (18 requested) atoms. Cycle 49: After refmac, R = 0.2079 (Rfree = 0.000) for 1026 atoms. Found 9 (18 requested) and removed 1 (18 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:12:04 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 44.13