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 1vjr-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.4-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/1vjr-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.4-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/1vjr-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.4-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 478 and 0 Target number of residues in the AU: 478 Target solvent content: 0.6349 Checking the provided sequence file Detected sequence length: 271 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 542 Adjusted target solvent content: 0.59 Input MTZ file: 1vjr-3.4-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: 93.998 93.998 160.365 90.000 90.000 90.000 Input sequence file: 1vjr-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4336 target number of atoms Had to go as low as 0.65 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. 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 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: 81.094 3.400 Wilson plot Bfac: 68.82 10438 reflections ( 99.93 % complete ) and 0 restraints for refining 4801 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3555 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3300 (Rfree = 0.000) for 4801 atoms. Found 36 (36 requested) and removed 148 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 2.96 Search for helices and strands: 0 residues in 0 chains, 4712 seeds are put forward NCS extension: 0 residues added, 4712 seeds are put forward Round 1: 175 peptides, 24 chains. Longest chain 16 peptides. Score 0.399 Round 2: 192 peptides, 22 chains. Longest chain 22 peptides. Score 0.461 Round 3: 207 peptides, 20 chains. Longest chain 38 peptides. Score 0.514 Round 4: 203 peptides, 19 chains. Longest chain 26 peptides. Score 0.516 Round 5: 196 peptides, 20 chains. Longest chain 27 peptides. Score 0.491 Taking the results from Round 4 Chains 19, Residues 184, Estimated correctness of the model 0.0 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10438 reflections ( 99.93 % complete ) and 7265 restraints for refining 3532 atoms. 6365 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3080 (Rfree = 0.000) for 3532 atoms. Found 26 (26 requested) and removed 66 (13 requested) atoms. Cycle 2: After refmac, R = 0.3061 (Rfree = 0.000) for 3391 atoms. Found 26 (26 requested) and removed 51 (13 requested) atoms. Cycle 3: After refmac, R = 0.2732 (Rfree = 0.000) for 3313 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 4: After refmac, R = 0.2755 (Rfree = 0.000) for 3276 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 5: After refmac, R = 0.2609 (Rfree = 0.000) for 3251 atoms. Found 22 (24 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.92 Search for helices and strands: 0 residues in 0 chains, 3333 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3369 seeds are put forward Round 1: 198 peptides, 24 chains. Longest chain 19 peptides. Score 0.453 Round 2: 213 peptides, 20 chains. Longest chain 21 peptides. Score 0.526 Round 3: 219 peptides, 26 chains. Longest chain 20 peptides. Score 0.478 Round 4: 221 peptides, 25 chains. Longest chain 33 peptides. Score 0.492 Round 5: 218 peptides, 24 chains. Longest chain 27 peptides. Score 0.496 Taking the results from Round 2 Chains 20, Residues 193, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10438 reflections ( 99.93 % complete ) and 6373 restraints for refining 3150 atoms. 5621 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2626 (Rfree = 0.000) for 3150 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 7: After refmac, R = 0.2500 (Rfree = 0.000) for 3125 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2647 (Rfree = 0.000) for 3117 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 9: After refmac, R = 0.2645 (Rfree = 0.000) for 3101 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 10: After refmac, R = 0.2510 (Rfree = 0.000) for 3083 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 3175 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3196 seeds are put forward Round 1: 195 peptides, 19 chains. Longest chain 21 peptides. Score 0.499 Round 2: 205 peptides, 20 chains. Longest chain 25 peptides. Score 0.510 Round 3: 208 peptides, 20 chains. Longest chain 27 peptides. Score 0.516 Round 4: 215 peptides, 23 chains. Longest chain 22 peptides. Score 0.500 Round 5: 216 peptides, 20 chains. Longest chain 24 peptides. Score 0.532 Taking the results from Round 5 Chains 20, Residues 196, Estimated correctness of the model 4.9 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10438 reflections ( 99.93 % complete ) and 5725 restraints for refining 3086 atoms. 4850 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2758 (Rfree = 0.000) for 3086 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Cycle 12: After refmac, R = 0.2653 (Rfree = 0.000) for 3052 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 13: After refmac, R = 0.2473 (Rfree = 0.000) for 3007 atoms. Found 22 (22 requested) and removed 49 (11 requested) atoms. Cycle 14: After refmac, R = 0.2216 (Rfree = 0.000) for 2957 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 15: After refmac, R = 0.2197 (Rfree = 0.000) for 2952 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 2.95 Search for helices and strands: 0 residues in 0 chains, 3054 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 3080 seeds are put forward Round 1: 216 peptides, 23 chains. Longest chain 23 peptides. Score 0.502 Round 2: 230 peptides, 23 chains. Longest chain 23 peptides. Score 0.531 Round 3: 226 peptides, 19 chains. Longest chain 29 peptides. Score 0.561 Round 4: 222 peptides, 21 chains. Longest chain 37 peptides. Score 0.534 Round 5: 220 peptides, 21 chains. Longest chain 27 peptides. Score 0.530 Taking the results from Round 3 Chains 21, Residues 207, Estimated correctness of the model 15.4 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10438 reflections ( 99.93 % complete ) and 5701 restraints for refining 2989 atoms. 4842 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2609 (Rfree = 0.000) for 2989 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 17: After refmac, R = 0.2377 (Rfree = 0.000) for 2965 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2273 (Rfree = 0.000) for 2944 atoms. Found 13 (22 requested) and removed 18 (11 requested) atoms. Cycle 19: After refmac, R = 0.2754 (Rfree = 0.000) for 2926 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2191 (Rfree = 0.000) for 2901 atoms. Found 14 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 2.92 Search for helices and strands: 0 residues in 0 chains, 2986 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3010 seeds are put forward Round 1: 201 peptides, 22 chains. Longest chain 26 peptides. Score 0.480 Round 2: 214 peptides, 25 chains. Longest chain 25 peptides. Score 0.477 Round 3: 222 peptides, 25 chains. Longest chain 23 peptides. Score 0.494 Round 4: 223 peptides, 22 chains. Longest chain 25 peptides. Score 0.526 Round 5: 233 peptides, 23 chains. Longest chain 32 peptides. Score 0.537 Taking the results from Round 5 Chains 26, Residues 210, Estimated correctness of the model 6.8 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10438 reflections ( 99.93 % complete ) and 5803 restraints for refining 3097 atoms. 4856 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2616 (Rfree = 0.000) for 3097 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2440 (Rfree = 0.000) for 3064 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2284 (Rfree = 0.000) for 3054 atoms. Found 18 (23 requested) and removed 27 (11 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 3036 atoms. Found 11 (22 requested) and removed 24 (11 requested) atoms. Cycle 25: After refmac, R = 0.2199 (Rfree = 0.000) for 3020 atoms. Found 9 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 3120 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3143 seeds are put forward Round 1: 227 peptides, 27 chains. Longest chain 37 peptides. Score 0.485 Round 2: 231 peptides, 22 chains. Longest chain 37 peptides. Score 0.542 Round 3: 246 peptides, 23 chains. Longest chain 26 peptides. Score 0.562 Round 4: 223 peptides, 22 chains. Longest chain 25 peptides. Score 0.526 Round 5: 241 peptides, 25 chains. Longest chain 41 peptides. Score 0.533 Taking the results from Round 3 Chains 27, Residues 223, Estimated correctness of the model 15.8 % 6 chains (95 residues) have been docked in sequence ------------------------------------------------------ 10438 reflections ( 99.93 % complete ) and 5436 restraints for refining 3249 atoms. 4149 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2438 (Rfree = 0.000) for 3249 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 27: After refmac, R = 0.2296 (Rfree = 0.000) for 3200 atoms. Found 11 (24 requested) and removed 27 (12 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2470 (Rfree = 0.000) for 3160 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 29: After refmac, R = 0.2265 (Rfree = 0.000) for 3115 atoms. Found 8 (23 requested) and removed 27 (11 requested) atoms. Cycle 30: After refmac, R = 0.2544 (Rfree = 0.000) for 3080 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 3177 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 3199 seeds are put forward Round 1: 194 peptides, 23 chains. Longest chain 20 peptides. Score 0.454 Round 2: 221 peptides, 25 chains. Longest chain 18 peptides. Score 0.492 Round 3: 222 peptides, 20 chains. Longest chain 32 peptides. Score 0.544 Round 4: 209 peptides, 21 chains. Longest chain 25 peptides. Score 0.508 Round 5: 209 peptides, 19 chains. Longest chain 27 peptides. Score 0.528 Taking the results from Round 3 Chains 21, Residues 202, Estimated correctness of the model 9.3 % 5 chains (79 residues) have been docked in sequence ------------------------------------------------------ 10438 reflections ( 99.93 % complete ) and 5644 restraints for refining 3136 atoms. 4533 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2608 (Rfree = 0.000) for 3136 atoms. Found 23 (23 requested) and removed 72 (11 requested) atoms. Cycle 32: After refmac, R = 0.2508 (Rfree = 0.000) for 3058 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2340 (Rfree = 0.000) for 3025 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 34: After refmac, R = 0.2500 (Rfree = 0.000) for 2994 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 35: After refmac, R = 0.2625 (Rfree = 0.000) for 2975 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 2.92 Search for helices and strands: 0 residues in 0 chains, 3038 seeds are put forward NCS extension: 65 residues added (4 deleted due to clashes), 3103 seeds are put forward Round 1: 194 peptides, 24 chains. Longest chain 21 peptides. Score 0.444 Round 2: 223 peptides, 19 chains. Longest chain 36 peptides. Score 0.556 Round 3: 217 peptides, 22 chains. Longest chain 30 peptides. Score 0.514 Round 4: 218 peptides, 22 chains. Longest chain 31 peptides. Score 0.516 Round 5: 215 peptides, 21 chains. Longest chain 26 peptides. Score 0.520 Taking the results from Round 2 Chains 21, Residues 204, Estimated correctness of the model 13.7 % 5 chains (90 residues) have been docked in sequence ------------------------------------------------------ 10438 reflections ( 99.93 % complete ) and 5244 restraints for refining 3058 atoms. 4089 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2728 (Rfree = 0.000) for 3058 atoms. Found 23 (23 requested) and removed 54 (11 requested) atoms. Cycle 37: After refmac, R = 0.2656 (Rfree = 0.000) for 3004 atoms. Found 22 (22 requested) and removed 43 (11 requested) atoms. Cycle 38: After refmac, R = 0.2876 (Rfree = 0.000) for 2951 atoms. Found 22 (22 requested) and removed 49 (11 requested) atoms. Cycle 39: After refmac, R = 0.2600 (Rfree = 0.000) for 2902 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 40: After refmac, R = 0.2249 (Rfree = 0.000) for 2879 atoms. Found 16 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 2987 seeds are put forward Round 1: 194 peptides, 22 chains. Longest chain 22 peptides. Score 0.465 Round 2: 223 peptides, 26 chains. Longest chain 23 peptides. Score 0.486 Round 3: 209 peptides, 22 chains. Longest chain 26 peptides. Score 0.498 Round 4: 218 peptides, 23 chains. Longest chain 22 peptides. Score 0.506 Round 5: 222 peptides, 23 chains. Longest chain 28 peptides. Score 0.514 Taking the results from Round 5 Chains 27, Residues 199, Estimated correctness of the model 0.0 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10438 reflections ( 99.93 % complete ) and 5446 restraints for refining 3021 atoms. 4443 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2469 (Rfree = 0.000) for 3021 atoms. Found 17 (22 requested) and removed 55 (11 requested) atoms. Cycle 42: After refmac, R = 0.2248 (Rfree = 0.000) for 2957 atoms. Found 15 (22 requested) and removed 27 (11 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2227 (Rfree = 0.000) for 2936 atoms. Found 15 (22 requested) and removed 22 (11 requested) atoms. Cycle 44: After refmac, R = 0.2114 (Rfree = 0.000) for 2922 atoms. Found 7 (22 requested) and removed 16 (11 requested) atoms. Cycle 45: After refmac, R = 0.2013 (Rfree = 0.000) for 2905 atoms. Found 4 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.95 Search for helices and strands: 0 residues in 0 chains, 2987 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3016 seeds are put forward Round 1: 207 peptides, 24 chains. Longest chain 31 peptides. Score 0.472 Round 2: 218 peptides, 23 chains. Longest chain 31 peptides. Score 0.506 Round 3: 215 peptides, 26 chains. Longest chain 22 peptides. Score 0.469 Round 4: 213 peptides, 20 chains. Longest chain 25 peptides. Score 0.526 Round 5: 215 peptides, 20 chains. Longest chain 36 peptides. Score 0.530 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 195, Estimated correctness of the model 4.2 % 4 chains (81 residues) have been docked in sequence Sequence coverage is 41 % Consider running further cycles of model building using 1vjr-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (195 residues) following loop building 4 chains (81 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10438 reflections ( 99.93 % complete ) and 5322 restraints for refining 3047 atoms. 4269 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2436 (Rfree = 0.000) for 3047 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2313 (Rfree = 0.000) for 3025 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2554 (Rfree = 0.000) for 3011 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2412 (Rfree = 0.000) for 2992 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 64.76