Sun 23 Dec 22:23:10 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 2pn2-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-1.9-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/2pn2-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-1.9-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 22:23:19 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/2pn2-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-1.9-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.5385 Checking the provided sequence file Detected sequence length: 155 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 155 Adjusted target solvent content: 0.40 Input MTZ file: 2pn2-1.9-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: 20 Cell parameters: 47.282 57.586 103.372 90.000 90.000 90.000 Input sequence file: 2pn2-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1240 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: 51.686 1.900 Wilson plot Bfac: 31.93 11413 reflections ( 99.42 % complete ) and 0 restraints for refining 1374 atoms. Observations/parameters ratio is 2.08 ------------------------------------------------------ Starting model: R = 0.3459 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2873 (Rfree = 0.000) for 1374 atoms. Found 29 (54 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.28 2.61 Round 1: 101 peptides, 9 chains. Longest chain 29 peptides. Score 0.780 Round 2: 108 peptides, 7 chains. Longest chain 34 peptides. Score 0.850 Round 3: 113 peptides, 8 chains. Longest chain 26 peptides. Score 0.849 Round 4: 118 peptides, 4 chains. Longest chain 48 peptides. Score 0.921 Round 5: 115 peptides, 7 chains. Longest chain 31 peptides. Score 0.872 Taking the results from Round 4 Chains 4, Residues 114, Estimated correctness of the model 99.4 % 3 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A 3 chains (116 residues) following loop building 2 chains (110 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1368 restraints for refining 1212 atoms. 490 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2976 (Rfree = 0.000) for 1212 atoms. Found 27 (48 requested) and removed 30 (24 requested) atoms. Cycle 2: After refmac, R = 0.2729 (Rfree = 0.000) for 1190 atoms. Found 41 (46 requested) and removed 23 (23 requested) atoms. Cycle 3: After refmac, R = 0.2657 (Rfree = 0.000) for 1204 atoms. Found 30 (45 requested) and removed 24 (23 requested) atoms. Cycle 4: After refmac, R = 0.2513 (Rfree = 0.000) for 1205 atoms. Found 26 (44 requested) and removed 23 (23 requested) atoms. Cycle 5: After refmac, R = 0.2433 (Rfree = 0.000) for 1202 atoms. Found 23 (43 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.19 2.51 Round 1: 117 peptides, 5 chains. Longest chain 48 peptides. Score 0.906 Round 2: 119 peptides, 5 chains. Longest chain 49 peptides. Score 0.910 Round 3: 121 peptides, 4 chains. Longest chain 49 peptides. Score 0.926 Round 4: 119 peptides, 6 chains. Longest chain 51 peptides. Score 0.897 Round 5: 117 peptides, 7 chains. Longest chain 38 peptides. Score 0.877 Taking the results from Round 3 Chains 4, Residues 117, Estimated correctness of the model 99.5 % 3 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 103 A 3 chains (119 residues) following loop building 2 chains (112 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1319 restraints for refining 1213 atoms. 420 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2639 (Rfree = 0.000) for 1213 atoms. Found 41 (43 requested) and removed 27 (24 requested) atoms. Cycle 7: After refmac, R = 0.2507 (Rfree = 0.000) for 1222 atoms. Found 17 (42 requested) and removed 25 (24 requested) atoms. Cycle 8: After refmac, R = 0.2383 (Rfree = 0.000) for 1212 atoms. Found 23 (41 requested) and removed 24 (24 requested) atoms. Cycle 9: After refmac, R = 0.2353 (Rfree = 0.000) for 1208 atoms. Found 28 (39 requested) and removed 24 (23 requested) atoms. Cycle 10: After refmac, R = 0.2348 (Rfree = 0.000) for 1210 atoms. Found 30 (39 requested) and removed 18 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.19 2.51 Round 1: 117 peptides, 5 chains. Longest chain 45 peptides. Score 0.906 Round 2: 122 peptides, 4 chains. Longest chain 48 peptides. Score 0.928 Round 3: 122 peptides, 5 chains. Longest chain 49 peptides. Score 0.916 Round 4: 122 peptides, 4 chains. Longest chain 47 peptides. Score 0.928 Round 5: 122 peptides, 4 chains. Longest chain 59 peptides. Score 0.928 Taking the results from Round 5 Chains 4, Residues 118, Estimated correctness of the model 99.5 % 4 chains (118 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 57 A Built loop between residues 75 A and 79 A Built loop between residues 136 A and 139 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1157 restraints for refining 1213 atoms. 153 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2699 (Rfree = 0.000) for 1213 atoms. Found 36 (38 requested) and removed 24 (24 requested) atoms. Cycle 12: After refmac, R = 0.2531 (Rfree = 0.000) for 1222 atoms. Found 27 (37 requested) and removed 24 (24 requested) atoms. Cycle 13: After refmac, R = 0.2434 (Rfree = 0.000) for 1222 atoms. Found 32 (36 requested) and removed 25 (24 requested) atoms. Cycle 14: After refmac, R = 0.2391 (Rfree = 0.000) for 1227 atoms. Found 24 (36 requested) and removed 24 (24 requested) atoms. Cycle 15: After refmac, R = 0.2374 (Rfree = 0.000) for 1223 atoms. Found 35 (35 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.20 2.52 Round 1: 123 peptides, 4 chains. Longest chain 48 peptides. Score 0.929 Round 2: 125 peptides, 4 chains. Longest chain 50 peptides. Score 0.933 Round 3: 121 peptides, 7 chains. Longest chain 30 peptides. Score 0.888 Round 4: 122 peptides, 5 chains. Longest chain 34 peptides. Score 0.916 Round 5: 122 peptides, 5 chains. Longest chain 48 peptides. Score 0.916 Taking the results from Round 2 Chains 5, Residues 121, Estimated correctness of the model 99.6 % 4 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A Built loop between residues 102 A and 105 A Built loop between residues 115 A and 120 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1159 restraints for refining 1213 atoms. 155 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2660 (Rfree = 0.000) for 1213 atoms. Found 28 (34 requested) and removed 25 (24 requested) atoms. Cycle 17: After refmac, R = 0.2471 (Rfree = 0.000) for 1213 atoms. Found 29 (33 requested) and removed 24 (24 requested) atoms. Cycle 18: After refmac, R = 0.2366 (Rfree = 0.000) for 1217 atoms. Found 16 (32 requested) and removed 24 (24 requested) atoms. Cycle 19: After refmac, R = 0.2292 (Rfree = 0.000) for 1207 atoms. Found 30 (30 requested) and removed 20 (23 requested) atoms. Cycle 20: After refmac, R = 0.2298 (Rfree = 0.000) for 1215 atoms. Found 25 (30 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.21 2.53 Round 1: 126 peptides, 3 chains. Longest chain 49 peptides. Score 0.944 Round 2: 128 peptides, 3 chains. Longest chain 50 peptides. Score 0.947 Round 3: 128 peptides, 4 chains. Longest chain 62 peptides. Score 0.937 Round 4: 129 peptides, 3 chains. Longest chain 50 peptides. Score 0.948 Round 5: 130 peptides, 2 chains. Longest chain 82 peptides. Score 0.958 Taking the results from Round 5 Chains 2, Residues 128, Estimated correctness of the model 99.8 % 2 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1138 restraints for refining 1213 atoms. 134 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2458 (Rfree = 0.000) for 1213 atoms. Found 23 (29 requested) and removed 26 (24 requested) atoms. Cycle 22: After refmac, R = 0.2322 (Rfree = 0.000) for 1207 atoms. Found 25 (27 requested) and removed 23 (23 requested) atoms. Cycle 23: After refmac, R = 0.2269 (Rfree = 0.000) for 1208 atoms. Found 19 (26 requested) and removed 23 (23 requested) atoms. Cycle 24: After refmac, R = 0.2245 (Rfree = 0.000) for 1203 atoms. Found 25 (25 requested) and removed 19 (23 requested) atoms. Cycle 25: After refmac, R = 0.2216 (Rfree = 0.000) for 1209 atoms. Found 24 (24 requested) and removed 17 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.21 2.53 Round 1: 127 peptides, 4 chains. Longest chain 50 peptides. Score 0.935 Round 2: 127 peptides, 4 chains. Longest chain 51 peptides. Score 0.935 Round 3: 127 peptides, 4 chains. Longest chain 42 peptides. Score 0.935 Round 4: 125 peptides, 5 chains. Longest chain 51 peptides. Score 0.921 Round 5: 128 peptides, 3 chains. Longest chain 83 peptides. Score 0.947 Taking the results from Round 5 Chains 4, Residues 125, Estimated correctness of the model 99.7 % 3 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 105 A Built loop between residues 114 A and 118 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1156 restraints for refining 1213 atoms. 152 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 1213 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 27: After refmac, R = 0.2304 (Rfree = 0.000) for 1211 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 1209 atoms. Found 12 (23 requested) and removed 13 (23 requested) atoms. Cycle 29: After refmac, R = 0.2222 (Rfree = 0.000) for 1206 atoms. Found 23 (23 requested) and removed 14 (23 requested) atoms. Cycle 30: After refmac, R = 0.2217 (Rfree = 0.000) for 1215 atoms. Found 16 (24 requested) and removed 22 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.21 2.53 Round 1: 127 peptides, 3 chains. Longest chain 51 peptides. Score 0.946 Round 2: 127 peptides, 3 chains. Longest chain 51 peptides. Score 0.946 Round 3: 126 peptides, 4 chains. Longest chain 48 peptides. Score 0.934 Round 4: 123 peptides, 7 chains. Longest chain 29 peptides. Score 0.893 Round 5: 123 peptides, 5 chains. Longest chain 51 peptides. Score 0.918 Taking the results from Round 2 Chains 4, Residues 124, Estimated correctness of the model 99.7 % 3 chains (123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 53 A Built loop between residues 101 A and 105 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1152 restraints for refining 1213 atoms. 148 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2520 (Rfree = 0.000) for 1213 atoms. Found 24 (24 requested) and removed 26 (24 requested) atoms. Cycle 32: After refmac, R = 0.2297 (Rfree = 0.000) for 1208 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 33: After refmac, R = 0.2266 (Rfree = 0.000) for 1206 atoms. Found 23 (23 requested) and removed 21 (23 requested) atoms. Cycle 34: After refmac, R = 0.2208 (Rfree = 0.000) for 1207 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 35: After refmac, R = 0.2218 (Rfree = 0.000) for 1205 atoms. Found 23 (23 requested) and removed 17 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.19 2.51 Round 1: 127 peptides, 3 chains. Longest chain 50 peptides. Score 0.946 Round 2: 127 peptides, 3 chains. Longest chain 51 peptides. Score 0.946 Round 3: 124 peptides, 3 chains. Longest chain 48 peptides. Score 0.942 Round 4: 127 peptides, 4 chains. Longest chain 51 peptides. Score 0.935 Round 5: 121 peptides, 5 chains. Longest chain 47 peptides. Score 0.914 Taking the results from Round 2 Chains 4, Residues 124, Estimated correctness of the model 99.7 % 3 chains (123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 53 A Built loop between residues 101 A and 105 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1146 restraints for refining 1213 atoms. 142 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2516 (Rfree = 0.000) for 1213 atoms. Found 24 (24 requested) and removed 25 (24 requested) atoms. Cycle 37: After refmac, R = 0.2331 (Rfree = 0.000) for 1212 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 38: After refmac, R = 0.2291 (Rfree = 0.000) for 1211 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 39: After refmac, R = 0.2223 (Rfree = 0.000) for 1210 atoms. Found 23 (23 requested) and removed 17 (23 requested) atoms. Cycle 40: After refmac, R = 0.2197 (Rfree = 0.000) for 1215 atoms. Found 24 (24 requested) and removed 21 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.17 2.48 Round 1: 125 peptides, 4 chains. Longest chain 50 peptides. Score 0.933 Round 2: 127 peptides, 3 chains. Longest chain 51 peptides. Score 0.946 Round 3: 125 peptides, 4 chains. Longest chain 48 peptides. Score 0.933 Round 4: 127 peptides, 3 chains. Longest chain 51 peptides. Score 0.946 Round 5: 126 peptides, 4 chains. Longest chain 48 peptides. Score 0.934 Taking the results from Round 4 Chains 4, Residues 124, Estimated correctness of the model 99.7 % 3 chains (123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 53 A Built loop between residues 101 A and 105 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11413 reflections ( 99.42 % complete ) and 1141 restraints for refining 1213 atoms. 137 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2521 (Rfree = 0.000) for 1213 atoms. Found 22 (24 requested) and removed 26 (24 requested) atoms. Cycle 42: After refmac, R = 0.2312 (Rfree = 0.000) for 1203 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.2240 (Rfree = 0.000) for 1203 atoms. Found 21 (23 requested) and removed 18 (23 requested) atoms. Cycle 44: After refmac, R = 0.2196 (Rfree = 0.000) for 1205 atoms. Found 21 (23 requested) and removed 17 (23 requested) atoms. Cycle 45: After refmac, R = 0.2167 (Rfree = 0.000) for 1209 atoms. Found 23 (23 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.20 2.52 Round 1: 125 peptides, 4 chains. Longest chain 50 peptides. Score 0.933 Round 2: 128 peptides, 3 chains. Longest chain 50 peptides. Score 0.947 Round 3: 126 peptides, 5 chains. Longest chain 48 peptides. Score 0.923 Round 4: 126 peptides, 5 chains. Longest chain 48 peptides. Score 0.923 Round 5: 125 peptides, 4 chains. Longest chain 48 peptides. Score 0.933 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 125, Estimated correctness of the model 99.7 % 3 chains (125 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 49 A and 53 A Built loop between residues 101 A and 104 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11413 reflections ( 99.42 % complete ) and 1004 restraints for refining 991 atoms. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2900 (Rfree = 0.000) for 991 atoms. Found 16 (19 requested) and removed 0 (19 requested) atoms. Cycle 47: After refmac, R = 0.2677 (Rfree = 0.000) for 991 atoms. Found 1 (19 requested) and removed 0 (19 requested) atoms. Cycle 48: After refmac, R = 0.2567 (Rfree = 0.000) for 991 atoms. Found 3 (19 requested) and removed 1 (19 requested) atoms. Cycle 49: After refmac, R = 0.2512 (Rfree = 0.000) for 991 atoms. TimeTaking 29.7