null Sun 23 Dec 22:23:02 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.2-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/1vjr-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.2-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 22:23:12 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.2-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.6203 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-3.2-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: 93.998 93.998 160.365 90.000 90.000 90.000 Input sequence file: 1vjr-3.2-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 3.200 Wilson plot Bfac: 61.41 12449 reflections ( 99.94 % complete ) and 0 restraints for refining 4811 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3522 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2578 (Rfree = 0.000) for 4811 atoms. Found 27 (43 requested) and removed 144 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.81 Search for helices and strands: 0 residues in 0 chains, 4738 seeds are put forward NCS extension: 0 residues added, 4738 seeds are put forward Round 1: 180 peptides, 24 chains. Longest chain 13 peptides. Score 0.411 Round 2: 204 peptides, 22 chains. Longest chain 22 peptides. Score 0.487 Round 3: 211 peptides, 20 chains. Longest chain 23 peptides. Score 0.522 Round 4: 213 peptides, 16 chains. Longest chain 32 peptides. Score 0.566 Round 5: 226 peptides, 20 chains. Longest chain 32 peptides. Score 0.552 Taking the results from Round 4 Chains 19, Residues 197, Estimated correctness of the model 31.6 % 5 chains (91 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 7587 restraints for refining 3843 atoms. 6447 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3267 (Rfree = 0.000) for 3843 atoms. Found 34 (34 requested) and removed 134 (17 requested) atoms. Cycle 2: After refmac, R = 0.2776 (Rfree = 0.000) for 3663 atoms. Found 33 (33 requested) and removed 62 (16 requested) atoms. Cycle 3: After refmac, R = 0.2688 (Rfree = 0.000) for 3585 atoms. Found 26 (32 requested) and removed 49 (16 requested) atoms. Cycle 4: After refmac, R = 0.2624 (Rfree = 0.000) for 3533 atoms. Found 28 (31 requested) and removed 39 (15 requested) atoms. Cycle 5: After refmac, R = 0.2579 (Rfree = 0.000) for 3487 atoms. Found 26 (31 requested) and removed 34 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.76 Search for helices and strands: 0 residues in 0 chains, 3545 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 3573 seeds are put forward Round 1: 213 peptides, 20 chains. Longest chain 23 peptides. Score 0.526 Round 2: 220 peptides, 20 chains. Longest chain 34 peptides. Score 0.540 Round 3: 211 peptides, 18 chains. Longest chain 33 peptides. Score 0.542 Round 4: 227 peptides, 20 chains. Longest chain 32 peptides. Score 0.554 Round 5: 217 peptides, 17 chains. Longest chain 29 peptides. Score 0.564 Taking the results from Round 5 Chains 19, Residues 200, Estimated correctness of the model 31.0 % 5 chains (97 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 5709 restraints for refining 3421 atoms. 4545 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2465 (Rfree = 0.000) for 3421 atoms. Found 30 (30 requested) and removed 45 (15 requested) atoms. Cycle 7: After refmac, R = 0.2260 (Rfree = 0.000) for 3355 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 8: After refmac, R = 0.2169 (Rfree = 0.000) for 3316 atoms. Found 20 (30 requested) and removed 30 (15 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 3296 atoms. Found 18 (29 requested) and removed 21 (14 requested) atoms. Cycle 10: After refmac, R = 0.2210 (Rfree = 0.000) for 3281 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.75 Search for helices and strands: 0 residues in 0 chains, 3350 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 3387 seeds are put forward Round 1: 227 peptides, 21 chains. Longest chain 33 peptides. Score 0.544 Round 2: 233 peptides, 17 chains. Longest chain 51 peptides. Score 0.593 Round 3: 225 peptides, 19 chains. Longest chain 33 peptides. Score 0.559 Round 4: 236 peptides, 20 chains. Longest chain 31 peptides. Score 0.571 Round 5: 227 peptides, 21 chains. Longest chain 29 peptides. Score 0.544 Taking the results from Round 2 Chains 18, Residues 216, Estimated correctness of the model 39.2 % 4 chains (138 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4706 restraints for refining 3326 atoms. 3293 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2554 (Rfree = 0.000) for 3326 atoms. Found 29 (29 requested) and removed 66 (14 requested) atoms. Cycle 12: After refmac, R = 0.2524 (Rfree = 0.000) for 3253 atoms. Found 29 (29 requested) and removed 40 (14 requested) atoms. Cycle 13: After refmac, R = 0.2482 (Rfree = 0.000) for 3203 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. Cycle 14: After refmac, R = 0.2478 (Rfree = 0.000) for 3170 atoms. Found 28 (28 requested) and removed 40 (14 requested) atoms. Cycle 15: After refmac, R = 0.2415 (Rfree = 0.000) for 3135 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.78 Search for helices and strands: 0 residues in 0 chains, 3198 seeds are put forward NCS extension: 64 residues added (4 deleted due to clashes), 3262 seeds are put forward Round 1: 219 peptides, 19 chains. Longest chain 23 peptides. Score 0.548 Round 2: 226 peptides, 19 chains. Longest chain 29 peptides. Score 0.561 Round 3: 221 peptides, 19 chains. Longest chain 20 peptides. Score 0.552 Round 4: 227 peptides, 17 chains. Longest chain 40 peptides. Score 0.582 Round 5: 238 peptides, 18 chains. Longest chain 39 peptides. Score 0.593 Taking the results from Round 5 Chains 21, Residues 220, Estimated correctness of the model 39.2 % 7 chains (124 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4619 restraints for refining 3176 atoms. 3273 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2520 (Rfree = 0.000) for 3176 atoms. Found 25 (28 requested) and removed 54 (14 requested) atoms. Cycle 17: After refmac, R = 0.2595 (Rfree = 0.000) for 3114 atoms. Found 28 (28 requested) and removed 53 (14 requested) atoms. Cycle 18: After refmac, R = 0.2408 (Rfree = 0.000) for 3069 atoms. Found 27 (27 requested) and removed 42 (13 requested) atoms. Cycle 19: After refmac, R = 0.2299 (Rfree = 0.000) for 3037 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 20: After refmac, R = 0.2391 (Rfree = 0.000) for 3022 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 2.74 Search for helices and strands: 0 residues in 0 chains, 3093 seeds are put forward NCS extension: 52 residues added (3 deleted due to clashes), 3145 seeds are put forward Round 1: 216 peptides, 17 chains. Longest chain 31 peptides. Score 0.562 Round 2: 218 peptides, 21 chains. Longest chain 27 peptides. Score 0.526 Round 3: 226 peptides, 14 chains. Longest chain 52 peptides. Score 0.608 Round 4: 210 peptides, 21 chains. Longest chain 33 peptides. Score 0.510 Round 5: 217 peptides, 20 chains. Longest chain 37 peptides. Score 0.534 Taking the results from Round 3 Chains 17, Residues 212, Estimated correctness of the model 43.2 % 5 chains (124 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4435 restraints for refining 3056 atoms. 3124 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2532 (Rfree = 0.000) for 3056 atoms. Found 27 (27 requested) and removed 48 (13 requested) atoms. Cycle 22: After refmac, R = 0.2517 (Rfree = 0.000) for 3003 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 23: After refmac, R = 0.2129 (Rfree = 0.000) for 2984 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 24: After refmac, R = 0.1967 (Rfree = 0.000) for 2977 atoms. Found 9 (26 requested) and removed 24 (13 requested) atoms. Cycle 25: After refmac, R = 0.1886 (Rfree = 0.000) for 2955 atoms. Found 12 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.76 Search for helices and strands: 0 residues in 0 chains, 3015 seeds are put forward NCS extension: 67 residues added (4 deleted due to clashes), 3082 seeds are put forward Round 1: 217 peptides, 17 chains. Longest chain 51 peptides. Score 0.564 Round 2: 231 peptides, 19 chains. Longest chain 34 peptides. Score 0.571 Round 3: 223 peptides, 15 chains. Longest chain 49 peptides. Score 0.594 Round 4: 204 peptides, 19 chains. Longest chain 27 peptides. Score 0.518 Round 5: 222 peptides, 17 chains. Longest chain 40 peptides. Score 0.573 Taking the results from Round 3 Chains 17, Residues 208, Estimated correctness of the model 39.4 % 4 chains (89 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4707 restraints for refining 3015 atoms. 3507 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2529 (Rfree = 0.000) for 3015 atoms. Found 27 (27 requested) and removed 53 (13 requested) atoms. Cycle 27: After refmac, R = 0.2639 (Rfree = 0.000) for 2970 atoms. Found 26 (26 requested) and removed 42 (13 requested) atoms. Cycle 28: After refmac, R = 0.2153 (Rfree = 0.000) for 2938 atoms. Found 17 (26 requested) and removed 30 (13 requested) atoms. Cycle 29: After refmac, R = 0.2085 (Rfree = 0.000) for 2912 atoms. Found 9 (26 requested) and removed 28 (13 requested) atoms. Cycle 30: After refmac, R = 0.2160 (Rfree = 0.000) for 2887 atoms. Found 23 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 2.74 Search for helices and strands: 0 residues in 0 chains, 2976 seeds are put forward NCS extension: 53 residues added (4 deleted due to clashes), 3029 seeds are put forward Round 1: 213 peptides, 19 chains. Longest chain 21 peptides. Score 0.536 Round 2: 224 peptides, 17 chains. Longest chain 30 peptides. Score 0.577 Round 3: 223 peptides, 17 chains. Longest chain 37 peptides. Score 0.575 Round 4: 219 peptides, 18 chains. Longest chain 27 peptides. Score 0.558 Round 5: 213 peptides, 20 chains. Longest chain 29 peptides. Score 0.526 Taking the results from Round 2 Chains 20, Residues 207, Estimated correctness of the model 34.7 % 6 chains (113 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4379 restraints for refining 2957 atoms. 3126 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2282 (Rfree = 0.000) for 2957 atoms. Found 22 (26 requested) and removed 48 (13 requested) atoms. Cycle 32: After refmac, R = 0.2422 (Rfree = 0.000) for 2918 atoms. Found 26 (26 requested) and removed 44 (13 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 2893 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 34: After refmac, R = 0.2017 (Rfree = 0.000) for 2876 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 35: After refmac, R = 0.1919 (Rfree = 0.000) for 2872 atoms. Found 9 (25 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.74 Search for helices and strands: 0 residues in 0 chains, 2937 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 2973 seeds are put forward Round 1: 217 peptides, 23 chains. Longest chain 25 peptides. Score 0.504 Round 2: 233 peptides, 18 chains. Longest chain 33 peptides. Score 0.584 Round 3: 226 peptides, 16 chains. Longest chain 29 peptides. Score 0.590 Round 4: 226 peptides, 20 chains. Longest chain 28 peptides. Score 0.552 Round 5: 232 peptides, 17 chains. Longest chain 34 peptides. Score 0.591 Taking the results from Round 5 Chains 18, Residues 215, Estimated correctness of the model 38.6 % 7 chains (143 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4114 restraints for refining 3040 atoms. 2693 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2462 (Rfree = 0.000) for 3040 atoms. Found 27 (27 requested) and removed 60 (13 requested) atoms. Cycle 37: After refmac, R = 0.2451 (Rfree = 0.000) for 2968 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 38: After refmac, R = 0.2351 (Rfree = 0.000) for 2933 atoms. Found 25 (26 requested) and removed 31 (13 requested) atoms. Cycle 39: After refmac, R = 0.2372 (Rfree = 0.000) for 2913 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 40: After refmac, R = 0.1887 (Rfree = 0.000) for 2888 atoms. Found 11 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.76 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2988 seeds are put forward Round 1: 216 peptides, 17 chains. Longest chain 34 peptides. Score 0.562 Round 2: 231 peptides, 19 chains. Longest chain 37 peptides. Score 0.571 Round 3: 222 peptides, 12 chains. Longest chain 68 peptides. Score 0.620 Round 4: 207 peptides, 19 chains. Longest chain 34 peptides. Score 0.524 Round 5: 227 peptides, 19 chains. Longest chain 30 peptides. Score 0.563 Taking the results from Round 3 Chains 15, Residues 210, Estimated correctness of the model 46.3 % 5 chains (139 residues) have been docked in sequence ------------------------------------------------------ 12449 reflections ( 99.94 % complete ) and 4227 restraints for refining 2992 atoms. 2855 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2660 (Rfree = 0.000) for 2992 atoms. Found 26 (26 requested) and removed 58 (13 requested) atoms. Cycle 42: After refmac, R = 0.2130 (Rfree = 0.000) for 2925 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 43: After refmac, R = 0.1931 (Rfree = 0.000) for 2900 atoms. Found 13 (26 requested) and removed 41 (13 requested) atoms. Cycle 44: After refmac, R = 0.1902 (Rfree = 0.000) for 2865 atoms. Found 15 (25 requested) and removed 19 (12 requested) atoms. Cycle 45: After refmac, R = 0.1864 (Rfree = 0.000) for 2856 atoms. Found 11 (25 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 2.76 Search for helices and strands: 0 residues in 0 chains, 2886 seeds are put forward NCS extension: 118 residues added (5 deleted due to clashes), 3004 seeds are put forward Round 1: 210 peptides, 16 chains. Longest chain 34 peptides. Score 0.560 Round 2: 225 peptides, 16 chains. Longest chain 37 peptides. Score 0.588 Round 3: 220 peptides, 15 chains. Longest chain 36 peptides. Score 0.588 Round 4: 215 peptides, 18 chains. Longest chain 25 peptides. Score 0.550 Round 5: 214 peptides, 13 chains. Longest chain 34 peptides. Score 0.596 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 201, Estimated correctness of the model 40.0 % 6 chains (121 residues) have been docked in sequence Sequence coverage is 59 % Consider running further cycles of model building using 1vjr-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 69 A and 76 A Built loop between residues 240 A and 244 A 14 chains (209 residues) following loop building 4 chains (130 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12449 reflections ( 99.94 % complete ) and 4190 restraints for refining 2918 atoms. 2842 conditional restraints added. Observations/parameters ratio is 1.07 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2489 (Rfree = 0.000) for 2918 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2419 (Rfree = 0.000) for 2888 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2436 (Rfree = 0.000) for 2854 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1894 (Rfree = 0.000) for 2833 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:24:20 GMT 2018 Job finished. TimeTaking 61.3 Used memory is bytes: 18071392