null Mon 24 Dec 07:30:21 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aam-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aam-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aam-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:30:25 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/noncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-parrot-noncs/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 3639 and 0 Target number of residues in the AU: 3639 Target solvent content: 0.6468 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-4.0-parrot-noncs.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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.55 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 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 169.060 4.000 Wilson plot Bfac: 76.13 46619 reflections ( 98.70 % complete ) and 0 restraints for refining 19944 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3461 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3074 (Rfree = 0.000) for 19944 atoms. Found 94 (94 requested) and removed 113 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 2.25 Search for helices and strands: 0 residues in 0 chains, 20229 seeds are put forward NCS extension: 0 residues added, 20229 seeds are put forward Round 1: 1026 peptides, 143 chains. Longest chain 21 peptides. Score 0.356 Round 2: 1096 peptides, 127 chains. Longest chain 29 peptides. Score 0.405 Round 3: 1148 peptides, 131 chains. Longest chain 27 peptides. Score 0.415 Round 4: 1165 peptides, 135 chains. Longest chain 24 peptides. Score 0.414 Round 5: 1150 peptides, 122 chains. Longest chain 27 peptides. Score 0.429 Taking the results from Round 5 Chains 122, Residues 1028, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4147 restraints for refining 16066 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2652 (Rfree = 0.000) for 16066 atoms. Found 76 (76 requested) and removed 48 (38 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 16094 atoms. Found 76 (76 requested) and removed 64 (38 requested) atoms. Cycle 3: After refmac, R = 0.2370 (Rfree = 0.000) for 16106 atoms. Found 76 (76 requested) and removed 74 (38 requested) atoms. Cycle 4: After refmac, R = 0.1964 (Rfree = 0.000) for 16108 atoms. Found 42 (76 requested) and removed 60 (38 requested) atoms. Cycle 5: After refmac, R = 0.1845 (Rfree = 0.000) for 16090 atoms. Found 23 (76 requested) and removed 53 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 2.20 Search for helices and strands: 0 residues in 0 chains, 16575 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 16604 seeds are put forward Round 1: 1144 peptides, 116 chains. Longest chain 43 peptides. Score 0.437 Round 2: 1228 peptides, 121 chains. Longest chain 35 peptides. Score 0.454 Round 3: 1221 peptides, 114 chains. Longest chain 36 peptides. Score 0.462 Round 4: 1172 peptides, 113 chains. Longest chain 30 peptides. Score 0.450 Round 5: 1207 peptides, 118 chains. Longest chain 33 peptides. Score 0.452 Taking the results from Round 3 Chains 119, Residues 1107, Estimated correctness of the model 0.0 % 6 chains (90 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4737 restraints for refining 15742 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2365 (Rfree = 0.000) for 15742 atoms. Found 74 (74 requested) and removed 49 (37 requested) atoms. Cycle 7: After refmac, R = 0.2242 (Rfree = 0.000) for 15767 atoms. Found 74 (74 requested) and removed 64 (37 requested) atoms. Cycle 8: After refmac, R = 0.2181 (Rfree = 0.000) for 15777 atoms. Found 74 (74 requested) and removed 76 (37 requested) atoms. Cycle 9: After refmac, R = 0.2121 (Rfree = 0.000) for 15775 atoms. Found 74 (74 requested) and removed 64 (37 requested) atoms. Cycle 10: After refmac, R = 0.2060 (Rfree = 0.000) for 15785 atoms. Found 75 (75 requested) and removed 65 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 2.19 Search for helices and strands: 0 residues in 0 chains, 16362 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 16377 seeds are put forward Round 1: 1206 peptides, 132 chains. Longest chain 39 peptides. Score 0.431 Round 2: 1254 peptides, 126 chains. Longest chain 37 peptides. Score 0.454 Round 3: 1247 peptides, 116 chains. Longest chain 41 peptides. Score 0.467 Round 4: 1215 peptides, 107 chains. Longest chain 48 peptides. Score 0.471 Round 5: 1234 peptides, 118 chains. Longest chain 51 peptides. Score 0.460 Taking the results from Round 4 Chains 113, Residues 1108, Estimated correctness of the model 0.0 % 6 chains (164 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 5144 restraints for refining 15928 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2312 (Rfree = 0.000) for 15928 atoms. Found 75 (75 requested) and removed 53 (37 requested) atoms. Cycle 12: After refmac, R = 0.2204 (Rfree = 0.000) for 15950 atoms. Found 75 (75 requested) and removed 62 (37 requested) atoms. Cycle 13: After refmac, R = 0.2125 (Rfree = 0.000) for 15963 atoms. Found 75 (75 requested) and removed 62 (37 requested) atoms. Cycle 14: After refmac, R = 0.1812 (Rfree = 0.000) for 15976 atoms. Found 30 (75 requested) and removed 56 (37 requested) atoms. Cycle 15: After refmac, R = 0.1775 (Rfree = 0.000) for 15950 atoms. Found 21 (75 requested) and removed 59 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 2.20 Search for helices and strands: 0 residues in 0 chains, 16423 seeds are put forward NCS extension: 51 residues added (2 deleted due to clashes), 16474 seeds are put forward Round 1: 1176 peptides, 141 chains. Longest chain 28 peptides. Score 0.408 Round 2: 1220 peptides, 120 chains. Longest chain 49 peptides. Score 0.453 Round 3: 1204 peptides, 123 chains. Longest chain 32 peptides. Score 0.444 Round 4: 1202 peptides, 135 chains. Longest chain 34 peptides. Score 0.425 Round 5: 1170 peptides, 113 chains. Longest chain 32 peptides. Score 0.449 Taking the results from Round 2 Chains 123, Residues 1100, Estimated correctness of the model 0.0 % 7 chains (137 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4891 restraints for refining 15793 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2270 (Rfree = 0.000) for 15793 atoms. Found 75 (75 requested) and removed 57 (37 requested) atoms. Cycle 17: After refmac, R = 0.2188 (Rfree = 0.000) for 15811 atoms. Found 75 (75 requested) and removed 61 (37 requested) atoms. Cycle 18: After refmac, R = 0.2141 (Rfree = 0.000) for 15825 atoms. Found 75 (75 requested) and removed 77 (37 requested) atoms. Cycle 19: After refmac, R = 0.2132 (Rfree = 0.000) for 15823 atoms. Found 75 (75 requested) and removed 75 (37 requested) atoms. Cycle 20: After refmac, R = 0.1806 (Rfree = 0.000) for 15823 atoms. Found 44 (75 requested) and removed 60 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 2.14 Search for helices and strands: 0 residues in 0 chains, 16343 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 16381 seeds are put forward Round 1: 1192 peptides, 150 chains. Longest chain 28 peptides. Score 0.399 Round 2: 1274 peptides, 148 chains. Longest chain 29 peptides. Score 0.427 Round 3: 1266 peptides, 145 chains. Longest chain 28 peptides. Score 0.429 Round 4: 1234 peptides, 132 chains. Longest chain 27 peptides. Score 0.439 Round 5: 1250 peptides, 137 chains. Longest chain 26 peptides. Score 0.436 Taking the results from Round 4 Chains 133, Residues 1102, Estimated correctness of the model 0.0 % 4 chains (68 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4630 restraints for refining 15729 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2433 (Rfree = 0.000) for 15729 atoms. Found 74 (74 requested) and removed 44 (37 requested) atoms. Cycle 22: After refmac, R = 0.2309 (Rfree = 0.000) for 15759 atoms. Found 74 (74 requested) and removed 44 (37 requested) atoms. Cycle 23: After refmac, R = 0.2228 (Rfree = 0.000) for 15789 atoms. Found 75 (75 requested) and removed 51 (37 requested) atoms. Cycle 24: After refmac, R = 0.2253 (Rfree = 0.000) for 15813 atoms. Found 75 (75 requested) and removed 54 (37 requested) atoms. Cycle 25: After refmac, R = 0.2246 (Rfree = 0.000) for 15834 atoms. Found 75 (75 requested) and removed 58 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 2.13 Search for helices and strands: 0 residues in 0 chains, 16417 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 16436 seeds are put forward Round 1: 1114 peptides, 146 chains. Longest chain 22 peptides. Score 0.380 Round 2: 1228 peptides, 145 chains. Longest chain 27 peptides. Score 0.418 Round 3: 1237 peptides, 141 chains. Longest chain 30 peptides. Score 0.427 Round 4: 1214 peptides, 140 chains. Longest chain 26 peptides. Score 0.421 Round 5: 1263 peptides, 140 chains. Longest chain 28 peptides. Score 0.436 Taking the results from Round 5 Chains 141, Residues 1123, Estimated correctness of the model 0.0 % 8 chains (82 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4729 restraints for refining 15915 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2511 (Rfree = 0.000) for 15915 atoms. Found 75 (75 requested) and removed 219 (37 requested) atoms. Cycle 27: After refmac, R = 0.2417 (Rfree = 0.000) for 15771 atoms. Found 74 (74 requested) and removed 50 (37 requested) atoms. Cycle 28: After refmac, R = 0.2408 (Rfree = 0.000) for 15795 atoms. Found 75 (75 requested) and removed 61 (37 requested) atoms. Cycle 29: After refmac, R = 0.2050 (Rfree = 0.000) for 15809 atoms. Found 42 (75 requested) and removed 48 (37 requested) atoms. Cycle 30: After refmac, R = 0.2089 (Rfree = 0.000) for 15803 atoms. Found 59 (75 requested) and removed 222 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.09 Search for helices and strands: 0 residues in 0 chains, 16194 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 16210 seeds are put forward Round 1: 1138 peptides, 174 chains. Longest chain 24 peptides. Score 0.344 Round 2: 1238 peptides, 152 chains. Longest chain 29 peptides. Score 0.410 Round 3: 1235 peptides, 155 chains. Longest chain 26 peptides. Score 0.405 Round 4: 1208 peptides, 141 chains. Longest chain 33 peptides. Score 0.418 Round 5: 1206 peptides, 151 chains. Longest chain 27 peptides. Score 0.402 Taking the results from Round 4 Chains 153, Residues 1067, Estimated correctness of the model 0.0 % 15 chains (171 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4864 restraints for refining 13394 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2720 (Rfree = 0.000) for 13394 atoms. Found 63 (63 requested) and removed 36 (31 requested) atoms. Cycle 32: After refmac, R = 0.2501 (Rfree = 0.000) for 13421 atoms. Found 63 (63 requested) and removed 36 (31 requested) atoms. Cycle 33: After refmac, R = 0.2477 (Rfree = 0.000) for 13448 atoms. Found 63 (63 requested) and removed 40 (31 requested) atoms. Cycle 34: After refmac, R = 0.2465 (Rfree = 0.000) for 13471 atoms. Found 64 (64 requested) and removed 51 (32 requested) atoms. Cycle 35: After refmac, R = 0.2196 (Rfree = 0.000) for 13484 atoms. Found 48 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 2.10 Search for helices and strands: 0 residues in 0 chains, 14069 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 14088 seeds are put forward Round 1: 1131 peptides, 170 chains. Longest chain 17 peptides. Score 0.348 Round 2: 1231 peptides, 153 chains. Longest chain 28 peptides. Score 0.407 Round 3: 1235 peptides, 160 chains. Longest chain 23 peptides. Score 0.397 Round 4: 1246 peptides, 156 chains. Longest chain 26 peptides. Score 0.407 Round 5: 1221 peptides, 146 chains. Longest chain 24 peptides. Score 0.414 Taking the results from Round 5 Chains 150, Residues 1075, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4338 restraints for refining 14692 atoms. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2699 (Rfree = 0.000) for 14692 atoms. Found 69 (69 requested) and removed 41 (34 requested) atoms. Cycle 37: After refmac, R = 0.2583 (Rfree = 0.000) for 14720 atoms. Found 69 (69 requested) and removed 41 (34 requested) atoms. Cycle 38: After refmac, R = 0.2546 (Rfree = 0.000) for 14748 atoms. Found 70 (70 requested) and removed 59 (35 requested) atoms. Cycle 39: After refmac, R = 0.2498 (Rfree = 0.000) for 14759 atoms. Found 70 (70 requested) and removed 43 (35 requested) atoms. Cycle 40: After refmac, R = 0.2540 (Rfree = 0.000) for 14786 atoms. Found 70 (70 requested) and removed 60 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 2.08 Search for helices and strands: 0 residues in 0 chains, 15400 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 15427 seeds are put forward Round 1: 1062 peptides, 169 chains. Longest chain 20 peptides. Score 0.326 Round 2: 1200 peptides, 159 chains. Longest chain 21 peptides. Score 0.388 Round 3: 1185 peptides, 157 chains. Longest chain 20 peptides. Score 0.386 Round 4: 1186 peptides, 153 chains. Longest chain 29 peptides. Score 0.393 Round 5: 1205 peptides, 154 chains. Longest chain 29 peptides. Score 0.397 Taking the results from Round 5 Chains 156, Residues 1051, Estimated correctness of the model 0.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4246 restraints for refining 15121 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2658 (Rfree = 0.000) for 15121 atoms. Found 71 (71 requested) and removed 44 (35 requested) atoms. Cycle 42: After refmac, R = 0.2599 (Rfree = 0.000) for 15148 atoms. Found 71 (71 requested) and removed 45 (35 requested) atoms. Cycle 43: After refmac, R = 0.2532 (Rfree = 0.000) for 15174 atoms. Found 72 (72 requested) and removed 54 (36 requested) atoms. Cycle 44: After refmac, R = 0.2526 (Rfree = 0.000) for 15192 atoms. Found 72 (72 requested) and removed 65 (36 requested) atoms. Cycle 45: After refmac, R = 0.2500 (Rfree = 0.000) for 15199 atoms. Found 72 (72 requested) and removed 53 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 2.11 Search for helices and strands: 0 residues in 0 chains, 15768 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 15785 seeds are put forward Round 1: 1010 peptides, 164 chains. Longest chain 18 peptides. Score 0.316 Round 2: 1158 peptides, 160 chains. Longest chain 24 peptides. Score 0.373 Round 3: 1204 peptides, 157 chains. Longest chain 35 peptides. Score 0.392 Round 4: 1211 peptides, 151 chains. Longest chain 23 peptides. Score 0.403 Round 5: 1203 peptides, 149 chains. Longest chain 36 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 156, Residues 1054, Estimated correctness of the model 0.0 % 6 chains (83 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2aam-4_warpNtrace.pdb as input Building loops using Loopy2018 156 chains (1054 residues) following loop building 6 chains (83 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 46619 reflections ( 98.70 % complete ) and 4470 restraints for refining 15141 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2685 (Rfree = 0.000) for 15141 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2534 (Rfree = 0.000) for 15106 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.2526 (Rfree = 0.000) for 15071 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.2487 (Rfree = 0.000) for 15036 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:40:04 GMT 2018 Job finished. TimeTaking 189.72 Used memory is bytes: 18321400